A careful review of your preferences may help. Command-comma will open it. Try every pane (left column) and see that none reference GNT-TD. Also check your startup (and any saved workspaces) to see you have references to that module.
You can also reinstall GNT-TD via Easy Install and in the Library Window move it to the very bottom of your text module list. It does not take up much space and it would eliminate the error messages. It is not elegant, but it would take care of the annoyance.
As for the observation about "Accordance should warn you..." this program has been around a long time and is mature (but not perfect). An earlier website description of Accordance was "Easy enough for beginners, powerful enough to be trusted by scholars" (or something to that effect). Any program this powerful is going to have controls and features that occasionally produce unexpected (and sometimes unwanted) behavior. That is part of the price one pays for this incredible tool. The Accordance folks have gone to great lengths to produce help files, create learning opportunities (seminars, blogs, podcasts, etc), and sponsor this forum (it is a great place to get problems like this addressed). Good as they are, they cannot anticipate every permutation of user (goals, skills, needs, ...).
Keep using the program. You will probably be very pleased with the investment (including the investment of time to learn how to use it).