The behavior you are seeing could be the result of a significant garbage 
colelction. You are not, by any chance, using the CMS collector? If so, if that 
collector gets behind in its duties, a full serial collection takes place, and 
that collection is usually very painful. One way to check this is to monitor 
the garbage collection data using -XX:+PrintHeapAtGC.

See my presentation at 
http://www.cecmg.de/doc/tagung_2007/agenda07/24-mai/2b3-peter-johnson/index.html

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