No easy answers, eh?
I would expect your PC running W2K to produce only very slightly lower sustainable frame rates than it would when running Win98, but I suppose that varies from system to system. The fact that the "stutter" occurs on a more or less regular basis would seem to indicate that it might be possible to adjust operational behavior of the system to eliminate the stutter.
I would expect the playback software to be capable of optimizing playback parameters, especially given the memory resources on your PC. I've seen clean video playback on Pentium 120s with 32 MB RAM, but only from hard drive. I've seen clean video playback from CD-ROM / DVD-ROM on 500 MHz PIIIs and faster, but most of them had less RAM than your PC. Assuming that clean video playback direct from CD under W2K isn't simply too much to expect from the PC you're using (and I don't think it is), I'd be checking to be sure that the system was trimmed down to the minimum with respect to services and concurrent apps.
I imagine you've already tried this, as well as the other things I've suggested. I'm just going over basic ground. Have you tried disabling all items in the user and common startup groups, HKLM Run, and HKCU Run locations of your registry to see if this improves matters?
Look in the Startup folder for any current user under whose logon you run games.
And look in the registry at:
HKEY_CURRENT_USER\Software\Microsoft\Windows NT\CurrentVersion\Windows:
Check the load REG_SZ and/or run REG_SZ values.
Also check these registry locations for items that start at boot time:
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Run
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunOnce
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunServices
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunServicesOnce
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\RunOnce
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\RunServices
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\RunServicesOnce
And have you examined your Services applet to see if you have any unnecessary services running automatically? Many services that run by default in W2K are not really necessary for proper function of a standalone workstation, or even for a system which makes only occasional use of network access. Of course an alternative to setting certain services to Manual or Disabled (Manual is safer unless you really KNOW you don't need the service.) is just to Stop them from the Services applet before you play a game. And if you wish to have a convenient way to enable / disable items in the aforementioned startup locations you might check Mike Lin's freeware applet Startup Control Panel at
http://www.mlin.net/StartupCPL.shtml
Forgive me if this is covering roads you've been down.
Regards,
Jim