Without more info, it sounds like you setup has a double bond in the system down line of the AFCI of the breakers. Check with local code first where the main bond needs to be. Make sure that there is no other neutral/ground bonds within your system. It could be built in the genset.
As for the AFCI tripping, I can't say for certain that a double bond would trip an AFCI. An AFCI and GFCI function differently. A double bond will definently trigger a GFCI but only from a second bond is down line from the divice
