Did you ever find a solution to this problem???
I am experiencing the a very similar problem in JBoss 3.2.6.

Everything runs fine for a couple days and then all of a sudden, the following 
Warning is outputted by JBoss indicating a timeout (upon Session Bean 
requesting info from a JMS Queue):


  | [org.jboss.tm.TransactionImpl] Transaction TransactionImpl:XidImpl 
[FormatId=257, GlobalId=<URL>//7466714, BranchQual=] timed out. 
status=STATUS_ACTIVE
  | 
  | 

I have looked at my deploy/transaction-service.xml file and see the following 
(I am curious if the SpecCompliant attribute has anything to do with this 
problem):


  | <?xml version="1.0" encoding="UTF-8"?>
  | <!-- $Id: transaction-service.xml,v 1.2.2.5 2003/10/05 15:37:24 starksm Exp 
$ -->
  | 
  | <server>
  | 
  |   <!-- ==================================================================== 
-->
  |   <!-- Transactions                                                         
-->
  |   <!-- ==================================================================== 
-->
  | 
  |   <!--
  |      | The CachedConnectionManager is used partly to relay started 
UserTransactions to
  |      | open connections so they may be enrolled in the new tx.
  |    -->
  |   <mbean code="org.jboss.resource.connectionmanager.CachedConnectionManager"
  |          name="jboss.jca:service=CachedConnectionManager">
  |     <depends 
optional-attribute-name="TransactionManagerServiceName">jboss:service=TransactionManager</depends>
  | 
  |     <!--SpecCompliant false means JBoss will close connections left open 
when you
  |         return from a method call and generate a loud warning.  
SpecCompliant true
  |         means JBoss will disconnect connection handles left open on return 
from a
  |         method call and reconnect them with an appropriate (security, tx)
  |         connection on the next call to the same object.-->
  |     <attribute name="SpecCompliant">false</attribute>
  | 
  |     <!-- Enable connection close debug monitoring -->
  |     <attribute name="Debug">true</attribute>
  | 
  |   </mbean>
  | 
  | </server>
  | 

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