Apple - Choosing the default application does not stay as default after reboot

I was doing it the wrong way like you try to for a long time and also have retreated to using RCDefaultApp in the past... but there's actually a way to do that natively which works.

Do the following:

1) right click your file 
2) choose "Get Info"
3) in the popup find the "Open with" strip (this is by default closed) and open it
4) from the drop down choose the program you want to open that type of file
5) click "Change all..."

And that's the correct way to do it

There's a great preference pane RCDefaultApp. It should do what you want.

RCDefaultApp is a Mac OS X 10.2 or higher preference pane that allows a user to set the default application used for various URL schemes, file extensions, file types, MIME types, and Uniform Type Identifiers (or UTIs; MacOS 10.4 only). MacOS X uses the extension and file type settings to choose the application when opening a file in Finder, while Safari and other applications use the URL and MIME type settings at other times for content not related to a file (such as an unknown URL protocol, or a media stream).