2) (If using Steam) Turn off the Steam Cloud. Right click on FTL in your game library and go to Properties, then in the Updates tab uncheck the box for cloud sync.
3) See if that fixed the problem
If that is the problem, then you're data will be lost But a helpful member of the fan community made this profile editor that will let you unlock any ships or achievements you've done! http://www.ftlgame.com/forum/viewtopic.php?f=7&t=2877
Sorry about this!
Matthew Davis, Subset Games Developer - If you're looking for tech support, you'll get help faster emailing directly, contact info here