Not compatible with ChatJax++
I'm going to need more information. At a minimum, the browser you're using, the OS, and user script manager.
I tried installing ChatJax++ in both Firefox+Greasemonkey and Chrome+Tampermonkey with the current released version of the script. I didn't experience this issue. Given that ChatJax++ only runs on chat pages and TNC doesn't run on chat pages, it's strange that there's any interaction.
I have seen some timing issues which can cause the script to fail under some conditions, which can be caused by changes in timing caused by having other scripts run. All issues I've seen along these lines have been fixed and a new version should be released shortly. However, these only showed up with specific other script which was both actively running on the page and the other script was doing things which caused Chrome/Tampermonkey to have some general issues (freeze the tab's UI for several seconds).
Thus, we can either try to track this down by you getting me some more info, allowing me to duplicate the problem, or you can wait a day, or two, to see if the new version fixes this issue. If you choose the latter case, we can revisit this after the new version is released.