Whoever mentioned the bug fix release, thank you! As may be ascertained from my prolonged absence, reinstalling the game with the new bug-fix patch fixed the problem.
A few fun hours later, I have 3 destroyers, 2 carriers, a bunch of frigates, a fuel tanker, and a tiny salvage cargo ship, plus around 240k, with 700 cargo space, 995 fuel storage, only 1.5 supply per turn in maint thanks to skills, only 10 fuel per turn thanks to skills, 60 marines, a good 800 friggin crew, 5 fighter squads of differing builds, and another 200k worth of junk in my cargo holds.
Oh, wait. I totally forgot about that massive cache of weapons, 200 fuel, 150 supplies, 95 machinery, and gods know what else in the storage bay of...
...Uhh...
Crap. Which of the thousand planets did I stash it on again? >_<
...Also, got an AWESOME mission from Eos Exodus to scan a derelict in orbit of a dead stargate: turned out to be sitting in a MASSIVE debris field with 10 or so derelicts. I filled my entire cargo, fuel tanks, and had to trash a good 400 metal and a bunch of weapons. :| Also, for some reason, I found a derelict with 300 fuel in it? Wat.
I'm actually glad I restarted. This is by far my most entertaining playthrough!
Ps, from starting over 20+ times, I noted the tutorial salvaged ships are randomly generated, as far as D-mods go. One playthrough they were TERRIBLE. I refuse to ever use a ship with a busted engine, as it slows down my entire fleet. Got the short stick a few times and got rid of ships, but this time I got lucky and had minimal D-mods of fairly useless variety.
Also... D-mods are damn useful if they're merely structural. So wait, less hull integrity I can easily fix with a hull mod (blast door, etc), and LESS supply expenditure/CR recovery costs!?
Shiiiiet, I don't know if I even want a non-D mod of my mainline ships.