Mike G.
Are your battery cables still connected? I'll bet they are. Try unhooking the cables and see if the problem stops. If the cycling is a internal overload in the charger that is tripping, the culprit could be the charger itself, a shorted cell or plate in the battery or a short in the charging system.
Your rig has had some generator issues, so there might be more to this than it appears. Is there any funny clicking sound coming from your voltage regulator that coincides with the tripping of the battery charger?
Stuart