Can you enable this in Hibernate to see if that solves the problem:

hibernate.cache.use_minimal_puts

Gavin and I have had a discussion on the potential problem. That, when using 
query cache, Hibernate will do a put on the JBossCache while retrieving from 
db. This can cause a long lock that resulting in TimeoutException.

If this were the case, we will need to provide a way to get around this.

-Ben

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