Yeah, I've also been frustrated by this one. I *think* it is a bug in JBoss AS. I actually havn't seen it for a while and had thought it was fixed in 4.0.4RC1.
If you can create any kind of reproducable testcase, report it in JBoss AS JIRA. I was never able to reproduce it reliably.
I've been trying to figure this bug out and might have come across some useful information...
I noticed that whenever I did *not* define a method for a stateful bean that had the @Remove @Destroy annotations, I could load the JSF page that referenced it once and each subsequent refresh caused the "Transaction already active."
I realize that this is definitely defined in the manual, but I am unsure if the lack of a destroy method should hang Seam, requiring a restart.
Not too sure if that helps at all.
If you can create an EAR, along with some instructions for how to make the error occur, that would be awesome.