Either is ok, but they are slighly easier to track on an individual basis when reported by GitHub.
Yup, the standard MFC code should be saving the layout to DDOBuilder.ini file. If its read only/or missing the access rights then the layout would reset every time the program is run.
There is a "known" issue in this area in that the stock MFC code does not quite restore windows to their exact locations on a new instance which I spent a long time trying to understand, but as the issue is right down in the core of the MFC code, I never quite found/understood what the solution needs to be.