Thanks for using NextGEN Gallery ColorBoxer!
ColorBoxer automatically sets and locks-in the necessary options at Gallery --> Options --> Effects upon activation, so as long as the plugin is currently activated, you should be fine.
For your reference, the following options are set...
Link Code line: class="mycolorbox" rel="%GALLERY_NAME%"
It sounds more like you're experiencing a conflict with another plugin, or scripts in your theme. To confirm this, you could try momentarily switching your theme to the built-in Twenty Twelve, and deactivate all plugins aside from NextGEN Gallery and ColorBoxer.
Additionally, if you'd like to post your URL, I'd be happy to take a look for you (you can email me if you'd prefer it remain private).
Hope this helps!