I believe this is a DirectX issue in that the fullscreen display always encompasses all the monitor space. If you had a program that made your second WoW runtime it would be wrapping it all in a overlay I would assume (ewww)

I use Ultramon/MultiMon at work, I cannot see how it would give you any WoW benefits other than making windowed mode WoW runtimes easier placement perhaps?

My instincts tell me your game video settings need to be castrated perhaps, 100 to 10fps is a pretty big hit. Also I am sure some of the Windows IT arch people could tell you how to performance monitor what is actually causing the 10fps and it should be trivial to determine.