More information on the issue, it's now happening on the 3.0.6044 release as well. Seems as though the first time Music Bee starts, I'm able to save changes. However, when I close by going to File>Exit and reopen a few seconds later, make changes and repeat, no changes are saved.
Once I re-run the installer, I am able to make changes that first time I open the program.
If it helps, I upgraded from release 2.5.5804.26036, not sure if my settings file may be broken from that.