Go into the Workspace menu (under Window I believe off the top of my head), and make sure only the drives you wish to record on are set as record drives and all else are set as either playback or transfer, depending on what you need those non-record drives to do. I had issues where some of my sessions were missing audio files after doing some clean up on my system drive (not my record drive). I went into Workspace and noticed that for months I had been recording to both my system drive and my record drive. The only thing I can think of is that when I upgraded to PT 8 from 7.4, this defaulted to setting all onboard drives as record, which I had not had set that way before PT 8. That, or it happened from deleting the Pro Tools Prefs folder.
So moral of the story, always check your Workspace when making system changes to make sure your audio is going where you want it, and only there.
