I believe that AFCI's tripping with some generator setups is a fairly common problem.
There was a post on another site a while back about how they will often trip at the moment transfer back to utility power takes place.
The diagnosis was that since the generator neutral is bonded at the generator frame and the utility side neutral is bonded at the service of the building, they became common at the transfer switch, creating the problem.
I think it was also noted that the same thing could occur with GFCI circuit breakers used in the panel for individual branch circuits. The tripping didn't occur with GFCI receptacles used down stream though, for obvious reasons.
As I recall, the suggested solution for this issue was to use a transfer switch that also switched and isolated the neutrals along with removing the neutral to frame bonding jumper at the generator, creating a true separately derived system.
I suppose if the garage door openers and refrigerator, etc... are protected by a single GFCI circuit breaker, changing to GFCI receptacles in the garage may at least solve that part of the problem anyway.
