Setup up Kaleidoscope as external diff tool in IntelliJ?
Let Kaleidoscope install it's command-line tool ksdiff (Menu - Kaleidoscope - Integration). Then use /usr/local/bin/ksdiff as "Path to executable" in the Jetbrains IDE. This works for me with PyCharm.
I was having the same problem, and my fix was, instead of pointing to the .app file, you need to browse the app and find the .sh file. In my case it was the diffmerge tool and it was like this:
/Applications/DiffMerge.app/Contents/MacOS/DiffMerge