In the past there have been many solutions to this type of problem. The first thing that you need to do is too begin spending some time changing over to Sesame.

In our experience, your reported problems have to do with Windows network protocols playing funny tricks on QA which is a DOS based 16bit program.  Make sure that your DB's are in a first generation. Make sure that when you recover a database, the actual data is clean and not corrupted. Many times when you recover a database, there remains damaged records. Check the contents use ALt + F6 to see in table view.

As far as the network, our experience is to make sure that your hubs are cleaned, checked often (loose connections at the jack, etc.). Make sure that your cabling is far from florescent lights (at least 2 feet).  Check you lan cards (they do go marginal and  have intermitten problems). Diagnose bottle necks.

You might say "yes I've done that",  to what I have quickly suggested, but recheck, experience is talking and human errors are the worst ones to spot.  Check your config files again (Win98). Since your file server is a Win98 PIII, I strongly recommend you replace that power supply if it is over two years old. I was the supervisor for Columbia Data Products until they moved to Delaware, we used to make power supplies (amongst other components) here for many manufacturers.

Good Luck