I have to look into this, but I think that because of the voice allocation, if you have two midi modules and they accept the same midi channel, that CCs received on that channel will only be output of the first midi module.
If you hold a midi note and then send another midi note (on a different midi channel), the CCs would then come out of the 2nd midi module. This is to associate CCs with notes such that MPE controllers are supported out of the box without needing any kind of special setup.
But anyway, I am going to work on the midi module quite soon anyway so I will double check this and come up with a fix.
In the meantime you probably have to use two different midi channels and put 8 CCs on each channel to use 16 CCs total.