Definitely apply WAS v3.5 fixpack 4. You might also want to check for specific e-fixes for memory leaks. We're running on W2k platform and have not had this problem.
WebSphere is horribly underdocumented if you are using it on the NT/2000 platform. IBM seems to be positioning their documentation (Redbooks) and phone support (Named Caller) so that WebSphere users are forced to purchase expensive IBM Global Services consulting in order to get off the ground...
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