Nevyrmoore: This is an error message you get if you quit without saving, due to the way the game was developed to work. As you play, the game itself actively modifies its own game data, with some changes being done straight away, and others being kept in system memory. All saving does is ensure that all the changes are physically written to the drive. The result of this is that if you ever quit without saving, you're left with a corrupted version of the game.
Unless you've kept backups of the games files (which is unlikely, seeing as this is an issue most only find out about after they've quit without saving), your only option is to choose the "Reset and Start Game" option in the Start Menu (run it as administrator, just in case), make sure you choose the "Save and Quit" option in future playthroughs, and make a backup copy of your game files each time you finish playing. Specifically, make copies of the STARA.COM and STARB.COM files, found in the C:\GOG Games\Starflight 1 and 2\Starflight 1\STARFLT\PLAY folder (if you installed to default).