We recently upgraded from an old Linux server running Samba to Server 2003. All of our clients are Windows 98 virtual machines, and heavily access the server for file services. ~95% of the time, there are no problems and all runs smoothly ... but at least once per day per machine, and sometimes much more frequently, the network shares become inaccessible from a program until the user clicks on the drive through explorer (which sometimes takes 10-20 seconds to access when the system is in this state). The problem is that soon after connectivity to the shares is lost, our legacy 16bit app typically freezes and locks Win98 ... which also corrupts data.
We've already disabled the autodisconnect feature on Server 2003, Win98 has all the patches, and the newest DSClient (with patches) is applied on Win98.
The only universal symptom we've noticed is that when a network share becomes inaccessible/frozen from DOS the shared drive shows up as 1.99GB instead of 135GB in explorer. For example:
Both servers have 135GB RAID arrays, and typically show up as 135GB. The moment the network share become patchy, we took this screen shot. This symptom seems to always happen right before the Win98 app comes down, can happen anywhere from 2 minutes to 8 hours after logging in, and occurs on all 38 of our Win98 VMs (some of which were built differently or use a different VM player just to see if that was the problem).
BTW - We cannot move to 2000/XP/etc for this legacy app because it is DOS-based and uses printer interrupts and such. We're in the process of writing a replacement, but that won't be ready for another 10-11 months.