so if the problem is most evident in full screen mode the simple work around would be: make desktop slightly bigger then the desired AC window size, run AC in windows mode at that resolution.

 

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even in windowed mode, it is choppy

 

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I got an ATI Radeon HD 4870 X2 and I get the same problem if I have any of the decal apps up on screen with exception of HUDS or Go Arrow. It's a problem with the way decal views are rendered and the way 2 (or more) gpus process the screens.
If there was a way for you to disable one of the 2 gpus via ATI's drivers (as far as I know there is no way unless you have a disable crossfire option), then the flickering will go away.

 

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This only happened to me when I had AC installed on a different hard drive than my decal plugins. I had to create a file under the C drive that wasnt program files like a Games folder and put everything under it.

 

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I would imagine it has to do with Decal taking precedence over AC for visuals. It doesn't happen for me when I'm on the main page of most Decal plugins, but traversing to sub-pages generates the choppiness. You can view similar choppiness if you run AC in a window, then click outside the window; usually the game runs choppy for one to a few minutes then corrects, running full speed even unselected. It's getting re-assigned in the visual update queue no?

-N.