You're saying that with something plugged into the serial port, the IR port still puts out IR (an emitter works when plugged in there), but if you remove the emitter and hard wire it to the DVD it does not work?

It sounds like there is some sort of voltage/current problem with the IR port on the RFX in that it puts out enough to drive a standard emitter but not enough to drive the DVD's hard wired Interface when the serial port is in use.