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Generally non-developer's PC is used lightly - no heavy weight applications occupying the RAM/CPU. However, a developer's PC is always pushed to the limits....so, along with the java apps you are mentioning, there might be other processes consuming CPU/RAM.
If you really want to compare these two PCs, then you got to restart them and just run the java app being tested. Have you tried this?
I haven't heard of Java storing logs. Even if it does, it will only eat up the hard disc space. I believe that Java app's performance is directly related to the available CPU time, RAM (heap size) and the efficiency of the programming.
Slow degradation of performance have multiple causes, related to infrastructure, memory or the application problems itself. I have tried to consolidate thought over it in this article may be of your help.
Please, don't resurrect old threads. I'm locking this one.