Hi - sorry about the trouble!
Looking at the attached log, it looks like the game *is* actually running modded - it's using a 64-bit version of Java rather than the 32 bit version the game comes with, and the vmparams file is modified. Could you try a clean install of the game to see if the problems persist? By "clean" I mean manually deleting the Starsector folder (after copying whatever you want to hold on to elsewhere - mods, saves, screenshots, logs, etc), re-downloading and then reinstalling the game.