I don't have any experience with AFCI's yet but have had fluorescent fixtures connected to GFCI's many times without any problems. I would guess you have some bad insulation somewhere or this circuit is sharing wires with another circuit. Maybe someone used the hot from this circuit and the neutral from another circuit (or the other way around) to feed a light or other load. Every time the homeowner turns on the load the breaker or GFCI would trip.
Curt
