Maybe I'm wrong but it seems CT can't cope with formatting at times.
If there is one tag in the source segment, one is often unable to reflect original format in case of differences in the word order. Right-click formatting does not contain many types of format (e.g. colourful font), besides it's more tedious way of formatting, intended, I guess, for introduction of non-source formats.
Would it be possible to provide the user with additional "non-mandatory" opening or closing tags?
Other than that, tags should be a bit more meaningful. I appreciate they are represented by numbers in subscript rather than icons that obscure actual text. But differentiating between opening and closing tags would be of benefit (e.g. diagonal closing tax just like in the case of righ-click formtting).
I know it's rubbish but brown colour rather than green for glossary resouruces in the mathboard would be consistent with default marking colour. Green should be colour for memory.