Did PAF report any problems when you ran the database through Check/Repair? I can try repairing it by running it through the Check/Repair function in Legacy 6.0, if you would like. It is reported to be better than PAF's Check/Repair function, and it would only take me a few minutes.
If other software is running without any glitches, and PAF is using other databases successfully, I suspect the problem is in that file. You can send me your file as an attachment to email@example.com Either a gedcom or a PAF backup would be fine, whichever you prefer.