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try activating the flag -verbose:class
and also, you yourself suggest, try either putting the jars in both WEB-INF/lib, or also in the system classpath to see if it's really a classloader/packaging issue.
Best thing really is to use a serious profiler (thread dumps is not enough) like yourkit or jrmc
In such a case then you need to try to increase Chunk and Max perm size and Max Heap size to make difference of accessing those request.
set JAVA_PROPERTIES=%JAVA_PROPERTIES% -Dweblogic.Chunksize=8192 -Dweblogic.utils.io.chunkpoolsize=8192
increased Maxpermsize to 1024m and Heap size as 3GB.
Check the results you will see grt difference.