It is distressingly common for application software to go into your system and change file properties so it becomes the application of choice instead of whatever you had before. Video software like Quicktime and Windows Media are particular stinkers, as are some image editors. Have you recently installed WordPad?

The best way to prevent this is to always use the "advanced" setting instead of the "most common" setting when installing new software. This usually brings up a screen sometime in the process asking if you want to change your preferences or not. If you get in trouble, as you found out you can use "properties" to do global changes to put things right.

I don't trust registry cleaners and almost never use them.