What version were you running before you updated HEAD? Alpha used different naming for CMR column names and if you don't specify them explicitly in jbosscmp-jdbc.xml and then upgrade from alpha, CMR lookups will fail.
If that's not the case, I have no trouble with CMR on head as of today.
I used beta1 before. I think this might be related to bug #544437. I will look into the bug to see if the behaviour is the same.
The behaviour in the mentioned bug looks like the problem I have, but my problem disappears when using commit option A (the SQL is generated, so it's not a caching thing going on). On the other hand, I can't seem to reproduce that behaviour (the disappearance of the bug) with the bugreport testcase and commit-option A.