Hello there!
In theory there should not be any conflict with other notetags, as the only thing the plugin does is run a regular expression on them to check if there is a template tag present. I'll take a look at it over the weekend to figure out what is happening.
Just a question though... the bubble tag is set in the template event, or in the source event that references the template with note tags?
I'll need that info to try and replicate the issue properly! :)