Okay I think I've gone as far as I can today. There's something funky that I screwed up with the CSS; something is not getting inherited properly anymore and the endphase orders windows have lost their team-specific colouring and are now solid black. For now, so be it, I'll mess with it later.
Additionally, I think I found a few more bugs with the flak cannons that I need to iron out myself; notably it seems to no longer be properly submitting orders. Sadly, I'll need to use the IDE to trace how they are being processed... sadly I'm away from that system for this week (ironically why I also had the time to work on it).
I may find time to work on it more this week, but if not, over the weekend or early next week certainly. In the meantime, please report any other odd behaviour that you guys see in End Phase because of these changes.
Sometime next week, I'll announce a new test game, with player-flown Capital ships.