I have a gut feeling that the problem is due to the loose footed mainsail. There is a difference in the loading on the boom when the mainsail is not attached; when the sail has a bolt rope on the boom the load is distributed linearly and the loads are higher at the luff than at the clew. When you put a loose footed main on, the load at the foot is now concentrated at the end of the boom and puts a much larger bending moment on the boom. This torque gets translated into a concentrated stress at the mainsheet bail. The failure point is going to be where the load is high and the strength is weakest; which would be at the thru-bolted bail.
I would contact Beneteau and ask if there has been any record of boom failures on the 390 and describe to them the problem and ask if they could tell you what the cause was (you might ask without telling them the main was loose-footed at first).