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I run two monitors under Windows 7. Each is plugged into a different video card. ISBoxer was working fine until I took a ~1 month hiatus. When I got back the first time I loaded up my 5 instances of WoW there was a half inch of desktop showing on the second monitor. My Window Layout shows no problems at all. I have no idea what the problem is.
Not really sure, but if you go to isboxer.com and click the link for the IRC.
Chances are good, the support will be a lot faster then a reply here.
Sounds like your desktop resolution on that monitor changed. Create a new Window Layout -- you can use the Window Layout Wizard from right clicking on Window Layouts. You can update the old Window Layout to use the new resolution if you select <Current Computer> from the drop-down on the Regions page
This was resolved via the ISBoxer IRC channel. One of the monitors was about 20 pixels offset from the one it was sitting next to.