Yeah, it appears that right now the Linux/OS X versions at least are in fact unbeatable, they always crash upon achieving victory. If it makes you feel any better, I lost a 6.5 hour run (loops + 1.5 hour battle against Providence, Monsoon, because game had slowed to 8 fps or so)
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On mitigation that might ease the sting a bit: in your case I'd say you should feel fully justified in just manually unlocking what you lost. In case you didn't know, achievements/unlocks are stored in simple text format in your Save.ini. Obviously you should avoid the temptation to unlock anything else as that'd detract from the enjoyment, but it's not cheating to specifically restore what you legitimately earned anyway but lost due to crash bugs. Details are in the wiki.
That said, you may want to simply take a break until 1.2.2 or 1.2.3 or whenever they get some polish to the Linux/Mac releases, it's kind of pointless to sink too much into them right now. Alternately, you could run the Windows version in a VM, or via Wine or whatever, it should be somewhat more stable. Sorry for your loss though, even giving yourself the achievements back isn't quite the same as getting the whole victory sequence and having them all appear as they should in-game
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