Deleting mimeTypes.rdf was a good thing to try. That helps when Firefox has inconsistent, conflicting, or corrupted entries which you can't clean up through the Options dialog. But there are some situations where it doesn't help, and a Reset won't help.

There are some cases in which a server sends a generic binary file type as the content-type (application/octet-stream). In this case, Firefox disregards your stated preference for the program to use because in many cases, this same content-type is used for executables such as program installers.

This is not a new issue, and the workarounds aren't always pretty. Here's a thread from last year with an extended discussion: 'do this automatically for files like this from now on' box greyed out. Anything there useful?

Thanks I'll check out the thread

My downloads are mostly of a common types (rar/zip). They behave the same across the board.

Allright the save file/open with issue seems to have saved itself. I'm still having trouble with getting torrent files to automatically open with utorrent without having to confirm the dialogue everytime. The box is tick but the popup shows each time.