I've not had any problems running jQuery Colorbox on ZC 1.5.5a!!

PHP5.6, jQuery 3.1.1, Colorbox 1.5.14, Wheelzoom 3.0.4, base template (Responsive Sheffield Blue v2.0)

Still in a test environment, just finished converting the template layout and starting the install/upgrading plugins. I use Colorbox for more than images so my install is a bit different as posted on GitHub.

I would suggest running uninstalls or try looking at your database and manually remove lost installs before trying it again. I noticed in RSB, the script for colorbox mobile wasn't where I use mine, but I didn't spend time looking for I removed it and installed my version.

When you refreshed admin, did colorbox config show up! Did you remove Slimbox?