Got Gimp 2.6 and finally managed to get it to work. In addition to the save issue, it also required making sure that I checked the box to "extend all visible layers" when doing it. Then saved without the export dialogue popping up. Then close and reopened (had a pink background when it reopened) and did my business with it and saved again, no export dialogue, and voila, it worked in game.
I listed the steps for anyone else thinking of modding the hoi counter strip.