I see a lot of creative work being done to get around the problem introduced by the latest critical patch. As people have accurately surmized, the media center remote actually alternates remote codes when a button is pressed. The media center IR driver can use this fact to debounce key presses. The effectively causes the behavior most folks are seeing in that the pronto (and likely other learning remotes) learn only one of the two codes and the IR driver will only accept it once because it is waiting for the alternate code so it can be sure a 2nd key press was made.
The good news is that there's a registry entry to enable/disable this debouncing behavior in the IR driver. All you need to do is disable it and the pronto and other universal remotes should work fine.