My guess is you have two version of GEDitCOM II on your computer and when you start by double clicking a file, it is launching the old one rather than the new one. MacOS seems to have a knack for picking the wrong one in this situation.
1. To confirm, you can check the version being run by choosing "About GEDitCOM II" in the "GEDitCOM II" menu. The current one will say version 1.8. When I installed 1.8 on a non-development computer, it does not come up with that notice.
2. To prevent this happening when double click a file, you should delete all old versions of GEDitCOM II on your computer. If you want to save old versions for any reasons, control click on them and compress to a zip file and then delete the source file. The zipped version will not get launched by MacOS, but can be expanded if ever needed.
John