I have two monitors, a 22" connected by DVI, and a 16" connected by VGA. Everything's working fine, but programs always open in the secondary monitor.
I followed the directions in this thread but they didn't work. The thread links to a tutorial at TheTechRepo, which tells how to create a script that lets the user choose which monitor xrandr should choose as primary. But after running the script, nothing changes - programs continue to open on the left. (Making the left monitor primary does move the panel to that monitor, but making the right-hand monitor primary only moves the panel back; programs still open on left.) I did re-boot after running the script, just in case it was necessary.
It's kind of annoying to have to turn on the auxiliary monitor and fetch programs over to the right-hand monitor when they open.