I use homebrew-cask to install my applications on OS X 10.9. Generally cask installs applications to /opt/homebrew-cask/Caskroom/ and then sym links them in /Applications. For example:

$ ls -lA /Applications/Kaleidoscope.app
 
lrwxr-xr-x  1 craig  admin    67B  3 Nov 23:14 /Applications/Kaleidoscope.app@ -> /opt/homebrew-cask/Caskroom/kaleidoscope/2.0.1_114/Kaleidoscope.app

In SourceTree, I open "Preferences" > "Diff" and set the "Visual Diff Tool" to "Kaleidoscope", when I try to close the "Preferences" screen I get an error stating:

Kaleidoscope Not Found

Kaleidoscope was not found on this Mac, please install it before selecting it as an external diff or merge tool.

EDIT
I originally guessed the issue was because Kaleidoscope was symlinked, but I just installed Kaleidoscope directly in /Applications and the issue is still present.