Set up a new beacon comment under Configure/Beacon/Comment and the check box remained on the new comment created after closing and restarting. So it's saving the .XML config.
BUT, THE THOUGHT OCCURRED TO ME: I was now inserting the .gpx and .pos files from a different directory than the APRSIS32 program directory. So when I inserted them from the same directory, they stayed upon closing the program. I presume that .XML config file only searches for them in the APRSIS32 program directory. That's why it worked in the past and not recently.
I don't know if there is a way to point to a different directory so the .XML file saves the configuration, but if not, no big deal now that I understand what happened. It was just easier for me to work with the files and backup the files in a separate directory.
Thanks for getting me to do some thinking.