Here I come in 5 years latter. I have been staying over at their place for the last week while my grandpa is recovering from surgery. I thought I would take a crack at the system. If you don't know, while you can download the Intelfile3 from the Niles website, you cannot use it as it says "You are not authorized". You have to have this IR capture device that dealers have to get passed that annoyance. What they do have is the firmware images for the IR Capture Station in that download from Intelfile3. After a bit of reverse engineering I found its off an older LPC2300 arm chip. Since the software looks for a comport, I figured its using one of those USB-to-Serial adapters. It also looks like when the capture station receives an escape (27) it immediately does some reset stuff and sends this string.
"# Bam IR Capture Unit 0.36 15Apr06\r\n"
I plugged in one of those duel USB serial port adapters I had around, connected them with a loop back adapter and fed a simple program that every time it received an escape, it would send that string.
EUREKA! I am now able to configure both the HT-MSU as well as the the GX2's. It just gets though the software part and doesn't help you if you need to have it learn a new remote, but at least you can update the firmware and change some devices around. I plan to build a Arduino device try to mimic it.
All in all, all this Niles stuff looks really hack-able. The Display wall panels run an ATMEGA128 with a DM9000 ethernet controler and 32k of static ram. I haven't popped open the Display's yet but might do it in the morning.