Ports 7-12 are combination RS232 or IR ports. If you are using IR emitters on those ports they must be sleaved emitters. What that means is that there is some heat shrink on part of the male connector so that the 3rd line on the RS232 female connector does not short to ground. When that happens the IR emitter will not work. URC sells a starter kit for the MSC 400 that includes these emitters.

The RFID is not the issue nor is the firmware.

DB