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It just isn't my month...

Well, the fixes are not fixing things.
I've been able to confirm with IBM that the specific problem that has cropped up is indemic to WebSphere 3.5 and 4.0.1.
WebSphere 5.0 does not have this problem, so we'll be migrating as soon as possible to WAS 5.0. I've been playing with WebSphere Studio and running our code base on a test 5.0 server with success, so I don't foresee any huge issues.
Stay tuned to see if I'm psychic or not.