You're analysis looks correct to me.

The synchronization is something to take up with the Hibernate folks on the 
hibernate.org forums, as its part of their general 2nd level cache management; 
not something controllable by JBoss Cache.

Inside isUpToDate(), before calling into JBC, the Hibernate/JBC integration 
layer suspends any ongoing tx and then resumes it on exit.  If your query 
involves lots of entities, that will happen multiple times. That could be 
expensive.

If you find that query caching slows down your app, don't do it. :)

Also, you mentioned a deadlock. Is there a deadlock?  Your discussion is of 
thread contention, which is not the same thing as a deadlock.

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