Short answer: The usual reason is poor configuration
But I'm afraid "why is my java system slow" is a massive question - you need to look at your entire system, from the bare metal it is probably running on, right the way through to how your people are (ab)using it.
Start with the simple question - what is slow, and how do you know it is slow? Are you comparing a multi-million issue server with another machine that's got 3 issues? Is it certain activities or users? (page loads, transitions, the admin screens, a single project, Dave from accounts is complaining in general, etc). Are there patterns like "ok at the weekend, but almost unusable at 3pm on Tuesdays".
"It's slow" is NOT a simple problem. You need to monitor and analyse this in detail.
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