I am noticing something to this effect as well. I just did a clean install of Windows 7 RC1 Build 7100 and I use InnerSpace with ISBoxer Suite. I have 5 accounts going with 4 'Slave' windows running on my second monitor. The 'slaves' are limited to 30 FPS in the background [they actually all sit at 25FPS?] by default but when I do focus on any 'slave' their FPS never really get higher than about 40FPS. I have an e8500 C2D processor with my 4 'slaves' all on the second core and my main on the first core. I initially set it up this way because I run QuestHelper on the main character and I figured since QH sucks so much CPU that it'd be best not to load up that core with more WoW instances. I haven't played around with the assignment of cores or have disabled all my addons to maybe see if something else is causing it but it's something I've been meaning to do since I did this fresh OS install. It's not a super big deal at the moment and I completely understand that my video card driver is in beta at the moment [as well as the OS I'm using ].

Some Specs:
Intel C2D e8500 @ 3GHz
8 GB RAM [Only using 3.5GB after an hour of boxing]
nVidia GTX 260 [216 Core Model ]
23" Monitor @ 1920x1080 [1x Main]
22" Monitor @ 1680x1020 [4x Slaves]

Video Settings on all characters are identical. Only settings that are turned up are View Distance [Halfway] and Environmental Detail [1/3rd of the way]. Everything else is set to as low as it can go or boxes are unchecked [Full Screen Glow/Specular Lighting/etc]. All characters have their resolution set to 1280x800 but of course the 'slaves' are squished down when they're divided into 4 quadrants on the second monitor.

Addons [All 5 Accounts]:
Bagnon
CT_Core
CT_BuffMod
CT_MailMod
ISBoxer
Jamba
ClearFont
TipTac
QuestHelper [1 Account Only]