It is related to http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6708580 as 
well as the entry on my blog. Its caused by switching to EXA by default in 
later Intel drivers, as well as poor X(Shm)GetImage performance.
This problem occurs when switching between hw-accaleration and 
software-rendering.

I contributed a small fix to completly disable hw accaleration as a
workarround which should avoid those worst-cases, it has been integrated
in JDK6u12b03 pre-release, would be great if you could give it a try:
http://download.java.net/jdk6/binaries/

A long-term solution would be to use the RENDER api, I am currently
working on a java2d backend based on RENDER. You can find some
information about it on my blog http://linuxhippy.blogspot.com/ as well
as http://78.31.67.79:8080/jxrender/.

- Clemens

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Intel Java Graphics Performace degradation in Intrepid
https://bugs.launchpad.net/bugs/288650
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