How to deal with java.io.EOFException error in Java application?

Recently a java application called Jin stopped working on my iMac under 10.6.8. On startup it gives a java.io.EOFException error. When I boot from a full backup on external hard disk, the program still works fine. It has run without problem for at least two years.
This program logs onto an online chess community called ICC (see chessclub.com) using a non-http protocol.
I have tried everything I can think of to repair the problem, including:
-- Reinstalling both Jin and Java
-- Playing with Java Preferences, in particular trying both 32-bit and 64-bit versions
-- Discarding a couple .plist files associated with Java and Jin
-- Repairing permissions
-- Replacing /usr/share/java/Tools with version from backup disk (I created a Smart Folder to find files recently changes, and these were the only java files that came up
I've run out of ideas. It seems to me that some obscure Java support file has been corrupted, but I have no idea what or where.
Is it a good idea to replace the entire /Library folder from backup, or is that going to cause a problem?
I have a very bad feeling about replacing /System from backup.

Please enable the following debug
CA server
/atg/epub/DeploymentServer
loggingDebug=true
/atg/deployment/DeploymentManager
loggingDebug=true
loggingThreadDebug=true
Agent Servers
/atg/epub/DeploymentAgent
loggingDebug=true
recreate and attach the full logs
++++
Thanks
Gareth
Please mark any update as "Correct Answer" or "Helpful Answer" if that update helps/answers your question, so that others can identify the Correct/helpful update between many updates.

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*clip*clip*clip*
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*clip*clip*clip*
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here.
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