The core has only ever had the USB-UIRT installed on it. My MCE receivers are only attached to the MD's. Basically after I re-installed, I downloaded the .tar file for the recompiled module, made the backup, and copied it over. Then I unplugged the UIRT then rebooted. After it was back up again, I plugged in the USB-UIRT, and of course it was automatically set up. I then proceeded to re-learn my dish, TV, and Roku Box IR bits, my receiver was in the list for the A/V.
After that, I did a reload, and that was it. Now the UIRT can receive from my MCE remotes just fine. While looking at the media director page in the web admin, it shows the MCE remote, but under IR receivers it says only the USB-UIRT.
I tested my pg-up pg-down and the channel up/down, as well as the up/down arrows on my harmony 880 remote (set to emulate MCE remote) and they all work fine in the cube and the channel guide.
I am not sure what you are experiencing, but a good place to start, would be to un-plug the uirt, and the mce blaster if plugged in, reboot the core/md, and after it is up, plug in the UIRT. See if that helps any.