Hi Jonas,
Did you ever find a solution for that problem? I guess we're hitting either the same or a very similar Bug. Configuration works as intended, but after shut/no shut of the Port the switchport trunk allow-multi-tag stops working and traffic with multiple tags is not forwarded by those ports anymore. Even more - removing this command from the interface makes it working again!!! Re-adding after removing that command from the interface does not change the forwarding behavior anymore.
I already opened a TAC-Case but didn't receive any valuable feedback by now...
Regars,
Michael