Power source-based switching is pretty buggy right now (especially in v2.2.1). I actually recommend turning it off if you're using Mountain Lion now, since the OS is much more friendly in terms of when it switches GPUs. You should just be able to use gfxCardStatus in Dynamic Switching mode and leave it there at this point, and trust that if an app kicks on the discrete GPU, it's probably doing it for good reason.
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Anything that accesses your iSight camera will kick the discrete GPU on as well, which is actually pretty reasonable, because the integrated GPU can struggle to keep up with iSight video + effects (if you're using Messages or Photo Booth or something).
If you keep Skype running all the time, though, I can see how it would be annoying. Truth be told I really despise Skype, so usually when people ask me to chat with it...I'll either tell them to call me, use AIM or Gtalk, or not talk to me at all. Heh.

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You bet.

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That makes a lot of sense. I'm adding something in v2.3 that makes sure only one GPU switch can be ordered at one time. It's very likely that the extremely small amount of time in between switches caused the graphical artifacts and rendering issues.