I just went from having 2 monitors to having 3 today. I had to reboot a couple times and have tried restarting the program as well as reimporting old settings I previous had backed up.

First off none of my taskbars would load until after I rebooted. Thats working fine now, it all loads up. However I have auto-hide turned on which will hide them the first time, but once I show it, it will never hide again until I restart the program. This happens both with the mouse and activating the start menu on any monitor, they will all flicker, and then the start menu pops up on a random monitor.
I've been trying so many different settings now I don't even remember what I started with.