The tweak software doesn't work with .net 2.0 - I found this on the web:
The third option is to simply disable the debounce feature of Media Center and use a single set of IR codes. I don't know why this isn't exposed in the settings screens in Media Center, because it's something that anyone with a learning remote will run into. To disable the debounce feature, you need to modify a single registry key. Standard registry editing rules apply...make sure you create a backup, know what you're doing, etc., etc. The key is called EnableDebounce, and from what I've read in various posts, it's found in the following locations:
For Media Center 2004: HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\idIr\Remotes\745a17a0-74d3-11d0-b6fe-00a0c90f57da
For Media Center 2005: HKEY_LOCAL_MACHINE\SYSTEM\ControlSet001\Services\HidIr\Remotes\745a17a0-74d3-11d0-b6fe-00a0c90f57da
So, fire up RegEdit, navigate to the appropriate key, and 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. After this modification, my universal remote now works like a charm, and I've added one more remote to the remote control graveyard behind my big screen TV.