You are right about the save game. We've identified an issue were Autosaves are being corrupted, which tends to make the game angry when showing the load or save dialog menus.
We'll have a fix in the upcoming 1.01 patch which should hopefully be public in a few days.
In the meantime fivetad's advice is correct, turn off the Steam Cloud syncing for Star Control (in Steam -> Star Control -> Properties -> Updates tab -> Steam Cloud) and then delete the most recent autosave. (Documents\My Games\Star Control\Saves)
It's possible that older autosaves have the issue as well. In that case keep deleting them till it works.
Sorry for the hassle.
Edit: Aww man, pshaw1 beat me to the punch