Mouse pauses every 2.5 seconds

Got a brand new 27 inch 3.06 Ghz Core 2 Duo iMac (2009). The magic mouse AND any USB mouse that I plug into it pauses at the same interval about every 2.5 seconds. It's just enough to screw up everything you are trying to do.
Tinkering with it, I have managed to figure out that it only does it when I use an external monitor plugged into the iMac...
I have an external 24 inch monitor plugged into the iMac to extend my desktop. The external monitor has 2 inputs (DVI and VGA). When I have both the iMac and the 24 inch monitor set to Mac (DVI), the mouse works just fine. But when the external monitor is set on the Windows machine (VGA), the mac mouse (Magic mouse or USB mouse) pauses every 2.5 seconds. I don't know why monitor input settings would cause the mouse to pause and I haven't seen any threads with the same problem. Any ideas?

The 27-inch iMac is the first (and only) Mac to make double-use of its video port.
I think you have already shown it is somehow related to the Mini DisplayPort, and you can easily reproduce the problem on-demand. Since Mac OS X still sees the second display, even when it is switched over to the VGA input, it may not be related to the new video input capability.
As a test, what happens if you put it into the state where the pausing is going on, then disconnect the adapter on the back of the iMac. I would assume iMac would pause for a second and reset to having only its built-in display, and the ongoing pausing issue would stop. Then, reconnect the adapter (display still set to VGA with active input). The iMac should reset to having the external display. Does the pausing issue start happening again?
Here's another test. With the display set to DVI, insert the Mac OS X installation disc and restart with the C key held down. This will force start up from the optical drive. When you get to Installer, you should see the default Desktop background on the external display, and that will indicate it is being recognized and used. You should be able to move your mouse cursor onto it, although the arrangement may be different. Now, do the thing that usually causes the pausing. When you are started up from a different system, does the pausing still occur?

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Mouse pauses every 2.5 seconds

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