I was having the same problem with Windows 7. I also found it necessary to remove some other registry entries including "arduino.exe." Sorry, I didn't make note of where the entries were, but I found then easily with a registry search.
EASY FIX TIP: If you don't want to be bothered making registry changes, you can work around the issue by renaming the new arduino.exe to something like arduino22.exe. Then you should be able to re-associate .pde files with the new version by the standard means (Right click file. -> Open with -> Choose default program...).