Hm, this file works fine on my computer. The only other thing I can think of is that the mate command you have is an old version, though I am not sure if that is even possible. Did you start using TextMate from this last version?
Are you closing the preferences window in Texniscope before trying? When you command-click in the Texniscope document, what exactly happens? Does the focus move to TextMate, or does it stay in Texniscope? If it goes back to TextMate, does it go to the right file, but wrong line number, or it doesn't even find the right file? Try using the ~/bin path instead.
Haris