Quite frankly, there's too many variables (and not nearly enough information) here to even attempt to pose a solution. You're going to need to do more analysis. It could be application related, server related, configuration related or a combination of the above.
I would also say that you are incorrect in assuming that there is no impact on your server, merely due to the fact that is a dual-proc, quad core system. Is the CPU load spread out across all the cores, or is it just pinning one core? If you hit (1) in top, what does it say per-core/cpu?
Until you figure it out though, you might consider writing a cron script that restarts the service (perhaps daily in off-hours), just in-case you are wrong about there being no impact to the server.
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