Single pole breaker in Transfer Switch trips on transfer to GEN position every time but only on Master Bedroom circuit, 5 others OK
You can't put GFCI, AFCI or MWBC circuits on transfer switches.

I'm referring to the flimsy 6, 8 or 10 circuit switches that let you flip each circuit to utility or gen individually. 

And you have both GFCI and MWBC. 

So, yeah, not gonna happen.  

That panel should have never been recommended to you. Unfortunately generator salesmen recommend that type because 50 years ago the things are designed to be an easy bolt-up to "any panel" precisely so that salesmen don't need to know anything about your panel.  However, technology has passed it up.  The concept is obsolete (and a bit dangerous) by modern standards.  The breakers aren't even very good. 

You need an interlocked subpanel, where you switch the whole subpanel from utility to gen, and the branch circuit breakers live in that subpanel. Those will work all day with AFCI, GFCI and MWBC. 



MWBC = Multi-Wire Branch Circuit, shared neutral. Requires common throw.
GFCI = Ground Fault Circuit Interruptor, looking for current differences between hot and neutral, which could shock people.
AFCI = Arc Fault Circuit Interruptor, looking for the "sound" of arcing, which starts fires.