I remember that the Fortress Mission (first one, that give you the Military rom) was broken. I tried to do it at 3 different Fortresses and the first stargate to reach was always far far away.I seem to recall digdug also mentioning some other odd and sundry wierd behaviors when play testing for me.
I even tried to reach one "far far away gate", after 10 minutes in autopilot mode with the godmodded Sapphire (that is also faster, if I remember correctly) I gave up.
I think this is easily fixed by adding a simple check for the distance of the stargates.
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Then there was a couple of cosmetic bugs, like the sign in St. Kathrine or Eridani without a stargate nearby.
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I really don't care if the savegame is inflated to 40+ Mb, I think that everybody can survive with savegames like that.
Maybe lags during loading and saving could arise on slow computers. This is maybe something to check.