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Server upgrade issue

One of our Domino servers was upgraded from 5.0.12 to 6.0.3, late I know but the environment only started the transition a couple of months ago. We came across our first server upgrade issue when a scheduled Java agent tried to run.

The agent manager was up and running fine but every time it tried to load a Java agent we got an error through the log file - java.lang.NoClassDefFoundError: java/util/zip/Inflater. Not something I had seen before so a trip to notes.net later and we had a solution. This is really a placeholder for myself for future reference but it does raise an interesting issue (to me at least). I must have upgraded 10 or 15 servers over the last few months and not seen any problems at all, it's exactly these sort of sporadic and non-repeatable problems which annoy me about computing. I realise that something must be different between this server and all of the other ones I work on, but how?

Not a biggie really, just exasperating.