Here is the fix for MCE and using another remote....

1)The Media Center uses a debounce style remote. That is, when you press
the same button twice the remote alternates the code is sends. There is
no way to record this into the remote. However there is a registry
change that will tell the Media Center to accept the same code twice in
a row.
There is a registry edit that will turn off the debounce.


HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\HidIr\Remotes\745a1
7a0-74d3-11d0-b6fe-00a0c90f57da]

You should see a DWORD key called "EnableDebounce". You'll notice it's
set to 1. Set it to 0 to disable debouncing. Experiment with this
value and see if you can resolve your issue.


Run Regedit to make the change, there is also another way to make this fix located in this site in the files section under microsoft,, Media Center Edition

You'll need to reboot the computer to have this registry change take
effect.

This will solve the problem and you will be able to use your remote. Also sometimes after updates are made to MCE you will have to make this change again as some updates seem to return the original setting.

Hope you understand this, if you need more help on how to do this I can detail this more.....