How can multiple kjs produce different results?

I have two kjs's running on a single (unclustered) machine. Now whenever I run the server the first kjs seems to be O.K the second however seems to just accept requests and not return them - I see thread add contiously added to the kjs.log and every other browser request will hang, if I disable the second kjs everything works o.k. Have have also noticed running top that this second kjs is constantly running consuming a minimum of 30%+ processor all the time.
Does anybody have any idea as to how the 2kjs's could behave differently considering they are using the same script parameters ?

need some more clues:
1. Is the behaviour specific to the VM, i.e if you were to disable kjs1 and only enbale kjs2 does the app behave correctly.
2. is is this behaviour specific to your app, i.e does fortune work on both engines.
3. are you limited by some backend resource like db, jms etc.

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