BigAndFat,
It's been a while, but I have seen cases where backups will fail because the PDOXUSRS.NET (and *.LCK) files still think they're in use, generally because someone forgot to turn their machine off (and Paradox is still active) or they're simply shutdown the PC without properly logging off.
I'm not sure it's a great strategy, but I once handled the first case by adding a scheduled event to everyone's machine to fire a custom program that would walk through the active applications and terminate them one by one before shutting down the PC. This was written in Delphi and used standard Windows API calls to accomplish this; it also had a thirty second timer that was started when the program started, just in case there really was someone at the keyboard. It was scheduled to fire about 20 minutes before the backup started.
The second case was handled two ways. First, extensive user training was performed to educate the users on the problems with shutting down their PC's with the power switch, as opposed to firing the shutdown process. They really responded when we told them that if they didn't do things properly, then their data wouldn't be backed up.
We then created a second Delphi program that looked for the PDOXUSRS.NET file and, if found, tried to delete it. If that failed, then we wrote a flag file into that directory. We then reworked the backup process to look for the flag file and, if found, skip that entire directory for that backup cycle (while dropping an email off to the admin containing the contents of the flag file. The flag file reported the user(s) that had the .NET file (and the .LCK files) open. The next day, the admin would visit the users, determine why they still had the .NET file open at 3:00 am, and (if needed) reinforce the basic lessons of turning off the PC properly.
It took a few weeks, but eventually, the problems stopped and we were able to get reliable backups of the databases.
The two Delphi programs didn't take that long to write and it might be easier than retooling your database applications to work with separated tables. (There are a host of data integrity issues associated with that approach.)
Hope this helps...
-- Lance