Java screen refresh problems

I've recently noticed problems running Java applications under 10.4.8, with the latest Java DST updates - Java version is reported as:
java version "1.5.0_07"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_07-164)
Java HotSpot(TM) Client VM (build 1.5.0_07-87, mixed mode, sharing)
I've seen problems running CLC Free Workbench (http://www.clcbio.com/free/) and Cytoscape (http://www.cytoscape.org/). When I launch the applications, the application window is not drawn correctly. Buttons and tabs are not drawn properly (edges misaligned or missing); some window elements fail entirely to display; menu labels may not be drawn, although clicking where the menu should be will drop down the menu. When I resize the window, redraw will typically fail entirely, although I can in some cases get elements to redraw by mousing over them. Basically, the applications are unusable.
When I launch Java Preferences or Java cache viewer, those windows also fail to draw, and I'm left looking at a blank rectangle.
A colleague running the same OS an Java versions has no problems on his Macbook - the applications display correctly. I'm running on a dual 1GHz PowerMac G4 (MDD).
Any suggestions as to how I can get my Java to draw to the screen?
Thanks,
Chris
Powermac G4 MDD, Dual 1GHz   Mac OS X (10.4.8)  

Following up on my own question - I took some advice I read in another thread, and created a new test account to see if the problem is specific to my account. Apparently it is as both problem applications display just fine when logged into the new account.
So, the question becomes why is my account having problems displaying Java apps? What can I flush/reset/delete to make things display properly again?
Powermac G4 MDD, Dual 1GHz Mac OS X (10.4.8)

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