ok, thanks for your input.
Oddly enough, we might have found a way that it works. Originally the Control monitor was a 1600x900 native monitor and the Main displays were 1080p, and every time we started up, the Main display would be off center and scaled wrong, we had to play with windows settings to make it work every time we started MS.
We put a 1080p monitor on the Control display and it SEEMS like having both resolutions for both displays match might have allowed us to work without issues. Now MS starts up and displays correctly on both. Time will tell, but so far this is the only time it has not messed up by doing this.
Thanks for your help.