Video Performance

Before ISBoxer, I used to run two windowed LOTRO clients at 2560x1600 at "Very High" graphics settings and just alt-tab between them. In crowded areas, I would have slow downs but the game was definitely playable. If I lowered one of the clients to "Medium", I would get fast frame rates and never experience any issues.
Using ISBoxer (Instant Swap On, 640x400 nested in front of 2560x1600), if I run both clients at "Very High", I consistently experience the following: Both monitors (I only use one for game windows) will flash black and then reload - it's almost identical to what happens when graphics drivers crash ("stopped responding and recovered..."). Most of the time I don't get any kind of error message though. After repeated tweaking, I can run a reliable session by having one client at "Medium" and one at "Low".
So I have one possible fix to the problem but I'm wondering why there would be such a big performance gap between running both clients in their own windows as opposed to running them together in Innerspace. In my old setup, didn't both windows continue to render in the background? I'm hoping that there isn't any real difference on GPU load and that I'm just missing some config option somewhere. Second, if this kind of performance drop is warranted, what options can I tweak to allow for higher graphics settings (would disabling Instant Swap help?) Thanks in advance!
(Hardware is E6850, 6GB RAM, GTX 285; per your post, cpu throttling is turned off; os is w7-64; nvidia drivers are up-to-date)