I am sure there is a reason why the software always starts in that resolution, but one possible solution is to run the program in Administrator mode. Simply right-click the executable file and choose Run as Administrator. Change your settings then repeat the process and launch the software again. I believe this is a situation where the software doesn't save the settings/configuration data due to the lack of security settings.
I've encountered the same issue with Winamp, where I configured it and then launched another instance and the program had its defaults on.