Trouble with Long Song in Logic

Has anybody ever run into this:
I have to record a real estate book on tape type deal, total of 2-3 hours, each song is set to tempo of 60 so I get more time. There are a total of about 200 takes, 2 tracks.
Here's the problem: when I close out the song and then load it back in, logic tells me that 37 files aren't referenced and when looking at the files they are blank!
After about a week of loading that same song up, the number of ref'd files goes down and then all of the files load up properly. ?????????
I am recording to a SATA drive on the G5 and I tried correcting permissions and even loading the project manager to see if that helps. It only happens when I'm doing a particularly long song file.
Any thoughts?
G5 1.6 Mac OS X (10.4.7)

Your problem could be related to this:
http://youtu.be/NIL071_uBo8
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