Good to know that you find the issue. and as far as I remember the default transaction time out is 5 seconds. Which IMO is ok. The Bitronix documentation mention 60 seconds here: http://docs.codehaus.org/display/BTM/Configuration, but I guess that the underlying DB is closing the connection after 5 seconds.
Can you share the stack trace? if everything goes ok inside the method invocation, it shoudn't take more than 5 secs at least not for the jBPM side.
Cheers