Well my success was short lived. Once I used the codes Mike sent me, I tested the unit from a short distance (a few feet and not aiming directly at the unit) and it worked fine.
When I sat a typical distance (10-12 feet) it no longer worked and I had the same problems I had before which was the switch either didn’t respond at all or it scrolled wildly through all the inputs landing on a random input. The remote that came with the switch works fine.
One thing I did notice is that when I tilt the MX3000 at 45 degrees towards me (aiming it essentially at the ceiling) the switch responds fine. When I aim the MX3000 directly at the switch, it exhibits the problems I stated before.
Despite not having my IR working flawlessly (everything works except the HDMI switch), I did install my MRF-250 this evening. It took a couple iterations (due to RF interference on ID 0) but I found a good spot and it works very well. I will say that the slightest amount of flickering on ID 0 prevented the MRF250 from working. Only when there was absolutely no interference did the unit work. I will also add that I had no problems with the placement of the emitters. First placement worked on all the components.
Any help on what I can do to make the HDMI switch cooperate would be greatly appreciated. I am currently trying several filter materials (electrical tape with pin holes, 3m foam tape, masking tape) between the emitter and the IR sensor to see if that helps.