It was pointed out to me by a cool user that there was a memory leak. I have now pinpointed it, but it appears to be a GameMaker bug (wonderful...)
In a recent update, I gave materials more power by letting them change GPU options on an individual basis. I reset this with gpu state functions, so you don't have to worry about conflicts. It turns out that gpu_get_state() (which is used by MMK_armature_draw) causes some kind of memory leak, even with the map destroyed. Even "ds_map_destroy(gpu_get_state())" causes the exact same leak!
If your materials don't change any GPU states, you can fix this by setting the value of "MMK_auto_handle_gpu_resets" to 0 or false by double clicking the extension in the resource view, double clicking "MMK_Models.gml" and opening macros and finding it in the list there. The latest version of GameMaker wasn't updating this value consistently for me, so try closing and re-opening the extension window to double-check that the value has changed.
I will report this bug to YoYoGames, so hopefully this will not be an issue in future!