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Thank you for your reply Charles,
I guess reducing performance is better than the memory footprint going out of control and garbage collection times increasing to an unacceptable value.
I could periodically close down and reopen the environment, but that feels like a hack :)
I will look more into the following: http://download.oracle.com/docs/cd/E17277_02/html/GettingStartedGuide/cachesize.html
The point is that the JE cache is intended to hold onto memory. That's what a cache does. The objects you mentioned earlier are in the cache. There isn't a leak, that we know of. If there isn't enough room left in the heap for efficient GC, reduce the size of the JE cache or increase the size of the heap.