Right, found some weird behaviour. If I save the FSM to my desired directory on a separate drive, it errors - and from then on, no matter where I try to save, I can't save the file. If, however, I restart the FSM Editor, and save in the FSM Editor folder (haven't explored other folders on the same drive, yet), I can save as much as I like - just so long as I don't save to another folder on another drive (or I have to restart again).
I think this applies to opening FSM's as well... only seems to work on the same drive. I imagine there's just an oversight made in passing command-line arguments to the compiler (probably simply missing quotes around pathnames).
Strange behaviour indeed!