Before I upgraded my PT rig, I could only close two projects before PT would quit. That sucked.
I've also had trouble with saving, like you are having.
My workaround was to consolidate all the takes as whole files with an identical start point, export them, and import them all into a new session. It was actually more than just a workaround, as I'll still do it to projects I'm mixing but didn't track, as the files are easier to navigate and work with. You also have the luxury of renaming each file as you'd like to see it's track name.
I have no evidence of this, but I think sometimes PT gets glitchy when there are a bunch of files linked to different sessions and areas on a disk. If you use one tracking session for basics, then build new sessions for overdubs for each song, your files can be all over the place.