I have not tried 2 screens but using the dual view in one screen takes a hit, perhaps that is a reason.
What happen if you run both screen at the same resolution, say 12 x 10?
Yep, I'm expecting it to take a bit of hit, but as a RTS it shouldn't be to noticeable.
It's not slowdown though. Ever send a 70Hz signal to a 60 or 65Hz display? The second screen looks a little like that, really bad screen tearing.
I'll try them both at the same res. using 16x12 on both screens, see if that makes any difference.