Shame that Kongregate's not working for you, though at least the game's out there, I suppose (and you'll be able to gradually figure out which places are the best to promote your game through trial and error).
I think there's always going to be people encountering bugs and giving bad reviews - it's a very fragile balance trying to get one game to work on such a wide variety of computers. I can appreciate how frustrating it can be when it's through no error of your own. Incase you're not already aware of it, F12 (or Ctrl Shift J on some computers) can bring up a very handing debugging console which might let you know where things are going wrong. I've discovered a 'CS Runtime is not defined' error in my own game, which may explain why it works once and needs the cache to be refreshed before working again (If I could just work out what the error actually means, I might be getting somewhere!)
If it's any consolation, I haven't discovered any problems or glitches with your game yet but will be sure to let you know if I do.
Right, let's try and recall a few things I said the last time before I was denied access to posting comments.
I really like the way the ship gets crippled by enemies, and you get that note that your crew are dying. I felt nice and helpless, though it might be a nice touch if you include the ability to send out a distress signal when close to death (which can, if lucky, summon allied ships to your aid. If less lucky, it could summon more pirates).
I still haven't encountered a second mission yet, as I got cut apart by pirates before I could locate another station. I'm keen to find out what sort of missions are on offer, and will definitely play more. Out of curiosity, is there a larger campaign style mssion at work behind the scenes, or is the game mostly about flying around trading, killing and upgrading?
Anyway, keep soldiering on! You've made a great game, and I'm sure some people will that when they've given it a longer play.