I’m using Yosemite 10.10.4 on a mid-2014 MBP with an HP 2009m monitor hooked up as a second display (not mirroring). When I have two Scrivener windows open, one on each display, CPU usage skyrockets, sometimes to 100%, and slows down the interface. Dragging both windows onto the same screen calms the CPU down to a normal level. Deselecting “Displays have separate spaces” in System Prefs does not affect this spike in CPU usage.
I’ll have to check this later on when I’m around a display, but in the meanwhile, so that I can more accurately test this, what precisely do you mean by “two Scrivener windows”? Are these all from the same project (e.g. QuickReference panels), or two whole project windows or something else?
The second question: you refer to the Displays have separate spaces option, do you use Spaces a lot, or OS X Full Screen mode on your project windows (I’m guessing not the latter since you mention dragging them around).