i had similar experience with Vienna ensemble pro, where VEP server was set to receive midi on 32 ports, each with 16 channels.
When in sam i instantiated VEP client plugin, sam was only able to send midi to 16 midi channels on port 1. In Sam midi track has only option to select channel, and it assumes it's on port 1.
For eg. this problem in Cubase was solved by introducing rack instruments, where every VSTI exposes its ports and channels (as i heard ).
Anyway, guys from Vienna solved this by making small 'event' plugin (mainly for Logic users), which you place on midi track.
As usual, on your midi track you choose midi out channel to VSTI, and in 'event' plugin you choose port. This routes incoming midi signal to VEP server to desired port.
Unfortunately for Independence, this works only in VEP, but what i actually wanted to say is that developers should extend midi track's I/O option to include ports,
not only channels on port 1.