yeah, unfortunately, IIRC this is a limitation with IPlug AU support at the moment and requires a rethink of how the channel IO string works and how AU buses are allocated to groups of channels. You can see my thoughts on the subject here
http://forum.cockos.com/showthread.php?t=97727
I think the same problem occurs with stock-IPlug (cockos version). You can't solve it with IsInChannelConnected() etc, it needs lower-level changes in the IPlugAU.cpp constructor. I haven't had the time to do it properly yet.