Program not saving changes other than "Autosave"

Question

I recently began a new music project. I have worked on the project for several days and regularly saved the changes. Until yesterday, whenever I would open up the FCE software, the project would automatically open (displaying the timeline, viewer, and canvas windows, etc.) and the cursor would be at the last place I'd done work.
I began a new interview project yesterday, and now it doesn't seem to "save" the changes that I make. I noticed that the last editing work that I had done on the music project hadn't been saved, in spite of the fact that I "manually" saved it (by doing either File>Save Project or File>Save all). I am able to recover recent versions through the "Autosave Vault."
In the "Autosave Vault," I can locate a version of the work--which is saved every 1/2 hour, but I cannot locate the sequence (or "project file" or "timeline") showing any changes which occurred after the hour (or 1/2 hour) that the autosave kept. Under preferences, I've put the captured footage and other items related to the project on an external firewire-connected hard drive.
Did I mess things up by not putting the project file in the "Documents" folder, or is there some other explanation?
I seem to be able to go back an manipulate and edit those files from the "Autosave" folder, but it is a tedious process unless I've finished working near the hour (or 1/2 hour time) "Autosave" time.
Any info/advice will be appreciated.
Thanks in advance,
Gary

Answer 1

Repairing permissions might solve the problem. It might: it is just an attempt that should never have any bad effect, and indeed often removes obstacles that prevent the application from working correctly. So you can try that at any time, even in the middle of a project.
The same applies to trashing preferences (not permissions); in this case the only side effect is that you must set your preferences again (scratch disk, easy setup, and any setting you changed in the User Preferences or System Settings).
But, see my previous answer, the first thing I suggest you to try (no side effects, very easy and fast) is "Save As" to a different volume. If that works, than clearly the problem is the health of the volume where you usually save your project files.
Piero