So this is admittedly on dosbox 0.74. With an un-modified config file (note that means ems and xms are both true), I can install from my "EA presents" cd (or any other means) and get the following file structure:
Folder: C:\dos\WCA
<DIR> Sat, 20 Nov 2010 11:43 3,949 KB GAMEDAT
Sat, 20 Nov 2010 11:43 17 KB ADLIB.ADV
Sat, 20 Nov 2010 11:43 14 KB HELP.TXT
Sat, 20 Nov 2010 11:48 0 KB HISCORE
Sat, 20 Nov 2010 11:43 11 KB MT32MPU.ADV
Sat, 20 Nov 2010 11:43 129 KB ORIGIN.EXE
Sat, 20 Nov 2010 11:43 1 KB README.TXT
Sat, 20 Nov 2010 11:43 5 KB SBDIG.ADV
Sat, 20 Nov 2010 11:43 0 KB WCA.CFG
Sat, 20 Nov 2010 11:43 281 KB WCA.EXE
Folder: C:\dos\WCA\GAMEDAT
Sat, 20 Nov 2010 11:43 21 KB ACADEMY.TIM
Sat, 20 Nov 2010 11:43 1 KB ARROW.VGA
Sat, 20 Nov 2010 11:44 4 KB COCKPIT.VGA
Sat, 20 Nov 2010 11:44 70 KB COMMUNIC.S12
Sat, 20 Nov 2010 11:44 76 KB COMMUNIC.S23
Sat, 20 Nov 2010 11:44 90 KB COMMUNIC.S24
Sat, 20 Nov 2010 11:44 89 KB COMMUNIC.S25
Sat, 20 Nov 2010 11:44 65 KB COMMUNIC.S27
Sat, 20 Nov 2010 11:43 1 KB COMMUNIC.T01
Sat, 20 Nov 2010 11:44 0 KB COMMUNIC.T12
Sat, 20 Nov 2010 11:44 0 KB COMMUNIC.T14
Sat, 20 Nov 2010 11:44 0 KB COMMUNIC.T15
Sat, 20 Nov 2010 11:44 0 KB COMMUNIC.T16
Sat, 20 Nov 2010 11:44 0 KB COMMUNIC.T17
Sat, 20 Nov 2010 11:44 0 KB COMMUNIC.T23
Sat, 20 Nov 2010 11:44 0 KB COMMUNIC.T24
Sat, 20 Nov 2010 11:44 0 KB COMMUNIC.T25
Sat, 20 Nov 2010 11:44 0 KB COMMUNIC.T27
Sat, 20 Nov 2010 11:44 1 KB COMMUNIC.YOU
Sat, 20 Nov 2010 11:44 54 KB CONFPANL.VGA
Sat, 20 Nov 2010 11:44 1 KB CREDITS.DAT
Sat, 20 Nov 2010 11:43 140 KB DISPLAY.PAK
Sat, 20 Nov 2010 11:43 6 KB FLAK.VGA
Sat, 20 Nov 2010 11:44 5 KB FONTS.FNT
Sat, 20 Nov 2010 11:44 0 KB FX.000
Sat, 20 Nov 2010 11:44 58 KB HISCORE.VGA
Sat, 20 Nov 2010 11:44 1 KB HOTRECT.PAK
Sat, 20 Nov 2010 11:44 0 KB INTEL.014
Sat, 20 Nov 2010 11:44 0 KB INTEL.015
Sat, 20 Nov 2010 11:44 0 KB INTEL.016
Sat, 20 Nov 2010 11:44 0 KB INTEL.017
Sat, 20 Nov 2010 11:44 0 KB INTELSHP.000
Sat, 20 Nov 2010 11:44 0 KB INTELSHP.001
Sat, 20 Nov 2010 11:44 0 KB INTELSHP.002
Sat, 20 Nov 2010 11:44 0 KB INTELSHP.003
Sat, 20 Nov 2010 11:44 0 KB INTELSHP.004
Sat, 20 Nov 2010 11:44 0 KB INTELSHP.005
Sat, 20 Nov 2010 11:44 0 KB INTELSHP.006
Sat, 20 Nov 2010 11:44 0 KB INTELSHP.007
Sat, 20 Nov 2010 11:44 0 KB INTELSHP.008
Sat, 20 Nov 2010 11:44 0 KB INTELSHP.009
Sat, 20 Nov 2010 11:44 0 KB INTELSHP.015
Sat, 20 Nov 2010 11:44 0 KB INTELSHP.041
Sat, 20 Nov 2010 11:44 0 KB INTELSHP.050
Sat, 20 Nov 2010 11:44 0 KB INTELSHP.051
Sat, 20 Nov 2010 11:44 247 KB INTRO.VGA
Sat, 20 Nov 2010 11:44 0 KB MESSAGE.V00
Sat, 20 Nov 2010 11:44 8 KB MISSILE.V00
Sat, 20 Nov 2010 11:44 8 KB MISSILE.V01
Sat, 20 Nov 2010 11:44 93 KB MUSIC.A00
Sat, 20 Nov 2010 11:44 122 KB MUSIC.R00
Sat, 20 Nov 2010 11:43 10 KB NWFONT.VGA
Sat, 20 Nov 2010 11:44 21 KB NUKE.VGA
Sat, 20 Nov 2010 11:44 144 KB OBJECTS.VGA
Sat, 20 Nov 2010 11:43 4 KB PALETTES.V00
Sat, 20 Nov 2010 11:44 67 KB PCSHIP.V00
Sat, 20 Nov 2010 11:44 60 KB PCSHIP.V01
Sat, 20 Nov 2010 11:44 72 KB PCSHIP.V02
Sat, 20 Nov 2010 11:44 63 KB PSHIP.V03
Sat, 20 Nov 2010 11:44 66 KB PCSHIP.V04
Sat, 20 Nov 2010 11:44 58 KB PCSHIP.V15
Sat, 20 Nov 2010 11:44 65 KB PCSHIP.V41
Sat, 20 Nov 2010 11:44 52 KB PCSHIP.V50
Sat, 20 Nov 2010 11:43 65 KB PCSHIP.V51
Sat, 20 Nov 2010 11:43 20 KB PILOTANM.VGA
Sat, 20 Nov 2010 11:44 57 KB PLANETS.V00
Sat, 20 Nov 2010 11:44 125 KB SHIP.V13
Sat, 20 Nov 2010 11:44 126 KB SHIP.V20
Sat, 20 Nov 2010 11:44 54 KB SHIP.V23
Sat, 20 Nov 2010 11:43 65 KB SIMCON.VGA
Sat, 20 Nov 2010 11:44 9 KB SIMFX.VGA
Sat, 20 Nov 2010 11:43 71 KB SIMROOM.VGA
Sat, 20 Nov 2010 11:43 21 KB STARS.VGA
Sat, 20 Nov 2010 11:44 5 KB STRAX.DRV
Sat, 20 Nov 2010 11:44 43 KB SUPERTM.DRV
Sat, 20 Nov 2010 11:44 232 KB TITLE.VGA
Sat, 20 Nov 2010 11:44 14 KB TM.DRV
Sat, 20 Nov 2010 11:44 31 KB TRANFX.VGA
Sat, 20 Nov 2010 11:44 51 KB VDU.V00
Sat, 20 Nov 2010 11:44 1 KB WAVEINFO.DAT
Sat, 20 Nov 2010 11:43 8 KB WINGMAN.VGA
Sat, 20 Nov 2010 11:44 60 KB XSHIP.V00
Sat, 20 Nov 2010 11:44 62 KB XSHIP.V01
Sat, 20 Nov 2010 11:44 72 KB XSHIP.V02
Sat, 20 Nov 2010 11:44 68 KB XSHIP.V03
Sat, 20 Nov 2010 11:43 61 KB XSHIP.V04
Sat, 20 Nov 2010 11:44 69 KB XSHIP.V05
Sat, 20 Nov 2010 11:44 71 KB XSHIP.V06
Sat, 20 Nov 2010 11:44 68 KB XSHIP.V07
Sat, 20 Nov 2010 11:44 62 KB XSHIP.V08
Sat, 20 Nov 2010 11:44 64 KB XSHIP.V09
Sat, 20 Nov 2010 11:44 83 KB XSHIP.V15
Sat, 20 Nov 2010 11:44 72 KB XSHIP.V20
Sat, 20 Nov 2010 11:44 72 KB XSHIP.V41
Sat, 20 Nov 2010 11:43 109 KB XSHIP.V50
Sat, 20 Nov 2010 11:44 115 KB XSHIP.V51
From that the game runs fine - no problems. if you still have issues then, theres something else going on. either your copy isn't installing properly (check the wca\gamedat folder matches the list above). also you have a couple of extra files in the root, config and install. Install.exe is probably the installer from the floppy version (renamed to origin.exe in the cd version)
my floppy version has the following file structure
Folder: C:\dos\wca2
<DIR> Sat, 20 Nov 2010 11:55 3,952 KB gamedat
<DIR> Sat, 20 Nov 2010 12:02 34 KB MISSIONS
Sat, 20 Nov 2010 11:54 17 KB adlib.adv
Sat, 20 Nov 2010 11:54 14 KB help.txt
Sat, 20 Nov 2010 11:54 0 KB hiscore
Sat, 20 Nov 2010 11:54 129 KB install.exe
Sat, 20 Nov 2010 11:54 11 KB mt32mpu.adv
Sat, 20 Nov 2010 11:54 1 KB readme.txt
Sat, 20 Nov 2010 11:54 5 KB sbdig.adv
Sat, 20 Nov 2010 11:54 0 KB wca.cfg
Sat, 20 Nov 2010 11:54 281 KB wca.exe
Folder: C:\dos\wca2\gamedat
Sat, 20 Nov 2010 11:54 21 KB academy.tim
Sat, 20 Nov 2010 11:54 1 KB arrow.vga
Sat, 20 Nov 2010 12:02 0 KB AS.0
Sat, 20 Nov 2010 12:02 0 KB AS.1
Sat, 20 Nov 2010 12:02 0 KB AS.2
Sat, 20 Nov 2010 12:02 0 KB AS.3
Sat, 20 Nov 2010 11:54 4 KB cockpit.vga
Sat, 20 Nov 2010 11:54 70 KB communic.s12
Sat, 20 Nov 2010 11:54 76 KB communic.s23
Sat, 20 Nov 2010 11:54 90 KB communic.s24
Sat, 20 Nov 2010 11:54 89 KB communic.s25
Sat, 20 Nov 2010 11:54 65 KB communic.s27
Sat, 20 Nov 2010 11:54 1 KB communic.t01
Sat, 20 Nov 2010 11:54 0 KB communic.t12
Sat, 20 Nov 2010 11:54 0 KB communic.t14
Sat, 20 Nov 2010 11:54 0 KB communic.t15
Sat, 20 Nov 2010 11:54 0 KB communic.t16
Sat, 20 Nov 2010 11:54 0 KB communic.t17
Sat, 20 Nov 2010 11:54 0 KB communic.t23
Sat, 20 Nov 2010 11:54 0 KB communic.t24
Sat, 20 Nov 2010 11:54 0 KB communic.t25
Sat, 20 Nov 2010 11:54 0 KB communic.t27
Sat, 20 Nov 2010 11:54 1 KB communic.you
Sat, 20 Nov 2010 11:54 54 KB confpanl.vga
Sat, 20 Nov 2010 11:54 1 KB credits.dat
Sat, 20 Nov 2010 11:54 140 KB display.pak
Sat, 20 Nov 2010 11:54 6 KB flak.vga
Sat, 20 Nov 2010 11:54 5 KB fonts.fnt
Sat, 20 Nov 2010 11:54 0 KB fx.000
Sat, 20 Nov 2010 11:54 58 KB hiscore.vga
Sat, 20 Nov 2010 11:54 1 KB hotrect.pak
Sat, 20 Nov 2010 11:54 0 KB intel.014
Sat, 20 Nov 2010 11:54 0 KB intel.015
Sat, 20 Nov 2010 11:54 0 KB intel.016
Sat, 20 Nov 2010 11:54 0 KB intel.017
Sat, 20 Nov 2010 11:54 0 KB intelshp.000
Sat, 20 Nov 2010 11:54 0 KB intelshp.001
Sat, 20 Nov 2010 11:54 0 KB intelshp.002
Sat, 20 Nov 2010 11:54 0 KB intelshp.003
Sat, 20 Nov 2010 11:54 0 KB intelshp.004
Sat, 20 Nov 2010 11:54 0 KB intelshp.005
Sat, 20 Nov 2010 11:54 0 KB intelshp.006
Sat, 20 Nov 2010 11:54 0 KB intelshp.007
Sat, 20 Nov 2010 11:54 0 KB intelshp.008
Sat, 20 Nov 2010 11:54 0 KB intelshp.009
Sat, 20 Nov 2010 11:54 0 KB intelshp.015
Sat, 20 Nov 2010 11:54 0 KB intelshp.041
Sat, 20 Nov 2010 11:54 0 KB intelshp.050
Sat, 20 Nov 2010 11:54 0 KB intelshp.051
Sat, 20 Nov 2010 11:54 247 KB intro.vga
Sat, 20 Nov 2010 11:54 0 KB message.v00
Sat, 20 Nov 2010 11:54 8 KB missile.v00
Sat, 20 Nov 2010 11:54 8 KB missile.v01
Sat, 20 Nov 2010 11:54 93 KB music.a00
Sat, 20 Nov 2010 11:54 122 KB music.r00
Sat, 20 Nov 2010 11:54 10 KB newfont.vga
Sat, 20 Nov 2010 11:54 21 KB nuke.vga
Sat, 20 Nov 2010 11:54 144 KB objects.vga
Sat, 20 Nov 2010 11:54 4 KB palettes.v00
Sat, 20 Nov 2010 11:54 67 KB pcship.v00
Sat, 20 Nov 2010 11:54 60 KB pcship.v01
Sat, 20 Nov 2010 11:54 72 KB pcship.v02
Sat, 20 Nov 2010 11:54 63 KB pcship.v03
Sat, 20 Nov 2010 11:54 66 KB pcship.v04
Sat, 20 Nov 2010 11:54 58 KB pcship.v15
Sat, 20 Nov 2010 11:54 65 KB pcship.v41
Sat, 20 Nov 2010 11:54 52 KB pcship.v50
Sat, 20 Nov 2010 11:54 65 KB pcship.v51
Sat, 20 Nov 2010 11:54 20 KB pilotanm.vga
Sat, 20 Nov 2010 11:54 57 KB planets.v00
Sat, 20 Nov 2010 11:54 125 KB ship.v13
Sat, 20 Nov 2010 11:54 126 KB ship.v20
Sat, 20 Nov 2010 11:54 54 KB ship.v23
Sat, 20 Nov 2010 11:54 65 KB simcon.vga
Sat, 20 Nov 2010 11:54 9 KB simfx.vga
Sat, 20 Nov 2010 11:54 71 KB simroom.vga
Sat, 20 Nov 2010 11:54 21 KB stars.vga
Sat, 20 Nov 2010 11:54 5 KB strax.drv
Sat, 20 Nov 2010 11:54 43 KB supertm.drv
Sat, 20 Nov 2010 11:54 232 KB title.vga
Sat, 20 Nov 2010 11:54 14 KB tm.drv
Sat, 20 Nov 2010 11:54 31 KB tranfx.vga
Sat, 20 Nov 2010 11:54 51 KB vdu.v00
Sat, 20 Nov 2010 11:54 1 KB waveinfo.dat
Sat, 20 Nov 2010 11:54 8 KB wingman.vga
Sat, 20 Nov 2010 11:54 60 KB xship.v00
Sat, 20 Nov 2010 11:54 62 KB xship.v01
Sat, 20 Nov 2010 11:54 72 KB xship.v02
Sat, 20 Nov 2010 11:54 68 KB xship.v03
Sat, 20 Nov 2010 11:54 61 KB xship.v04
Sat, 20 Nov 2010 11:54 69 KB xship.v05
Sat, 20 Nov 2010 11:54 71 KB xship.v06
Sat, 20 Nov 2010 11:54 68 KB xship.v07
Sat, 20 Nov 2010 11:54 62 KB xship.v08
Sat, 20 Nov 2010 11:54 64 KB xship.v09
Sat, 20 Nov 2010 11:54 83 KB xship.v15
Sat, 20 Nov 2010 11:54 72 KB xship.v20
Sat, 20 Nov 2010 11:54 72 KB xship.v41
Sat, 20 Nov 2010 11:54 109 KB xship.v50
Sat, 20 Nov 2010 11:54 115 KB xship.v51
Hope this is some help!