Hi Jimbo,
Could you post some picks? It sounds like it should work but doesn't, so some pics may give us a better idea of what is happening. If what you are saying is that both flap servo's work separately on the flap channel, but not with the Y. But the flap servo's work with the same Y hooked up to the aileron slot. Then the only thing I can think of is the receiver is not putting out enough power on the flap channel?
Calvi