I have fixed the problem. I had a variable name mismatch and rather than issuing an error, it just got rid of the input port. Once I used the correct name, the input port remained.
There is an additional problem that I encountered and that is that you cannot put the CAN transmit block for this device into a masked subsystem. The vehicle network toolkit has this same problem and it has a bug report out on it. Can anyone verify that this is indeed a bug in the xPC CAN transmit for softing CAN-AC2-PCI. When you mask the subsystem it is in, and try to use the variable name of a mask parameter for the identifier in the CAN transmit, it gives the following error "undefined function or variable".