I just spent another 20 minutes messing around with this problem and discovered a few things.
I set the MX3000 back to IR only for the HDMI switch. I generally sit around 10-12 feet from the TV (and switch). When I aim the MX3000 directly at the switch there is absolutely no reponse. When I tilt the remote back 45 degrees it works about 80% of the time. I just tried the MX3000 aimed straight up towards the ceiling (bottom of the MX3000 facing the switch) and it works 100% of the time! That led me to believe that either the IR signal from the MX3000 is too strong or the IR sensor on the switch is too sensitive. I then moved back about 20 feet from the switch and aimed the MX3000 directly at the switch and it worked 100% of the time. Im not an IR expert but I think that would validate the theory that the IR signal is too strong or the switch is too sensitive. When I aim the MX3000 in any other direction other than directly at the switch for 20' away, there is no response.
Ive tried putting tape on the emitter to cut the IR signal. I even tried that 3M foam double sided tape and there is not response. Is there any other way to cut the emitter signal?
Given that the MX3000 IR and IR emitters work with all my other components, I can assume the switch IR sensor is too sensitive and its not that the MX3000 IR signal being too strong? In which case, I would send back the switch for a new one and see if that works any better.