You're using JBossTS with Spring?
Yes I am using JbossTS with Spring.
At this time we haven't tried JBossTS within Spring. However, it would seem that your connectionisn't known to the transaction manager and hence all work you're doing on it (through to MySQL) is happening immediately (i.e., autocommit is still true). If the TM knew about your connection then it would turn autocommit off and explicitly call commit (or rollback) when the transaction terminates.
You may find http://www.javaworld.com/javaworld/jw-04-2007/jw-04-xa.html?page=1 useful.