Some programmable remote control will not work with Microsoft Media Center. You can use the following registry key fix and avoid paying $$$ for a new Vista certified remote.
For Media Center 2004: HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\idIr\Remotes\745a17a0-74d3-11d0-b6fe-00a0c90f57da
For Media Center 2005 and above : HKEY_LOCAL_MACHINE\SYSTEM\ControlSet001\Services\HidIr\Remotes\745a17a0-74d3-11d0-b6fe-00a0c90f57da
Change the EnableDebounce value from 1 (its default setting) to 0. Note that you’ll have to reboot your system for this change to take effect.