Noticed that the FPS in different windows is different at first, it takes up to 2 seconds to reach the maximum (after switch).
The FPS meter is showing average FPS over a number of elapsed frames. Default settings will put the foreground window at 60 fps and background windows at 30 fps, so at the instant you switch windows, it will indeed show a different number. If you want it to always be the same, you can set the foreground and background settings both to 30 for example, during the Quick Setup Wizard, or by using the CPU Strategy Wizard.
edit: I am using 1600x900 default resolution; also i just performed the "mouse out of sync" test that you have suggested (moving the mouse to the four corners of the screen) and i am pretty sure it's out of sync. To the left it seems fine, but to the right the cursor disappears off the 2nd client. It is off by at least 3-4 millimeters, maybe more.
Unless you have the game windows in full screen mode, I guarantee you they are not in 1600x900 resolution with this configuration. Your Window Layout has it at 1440x720, so they are supposed to all be at 1440x720.
The fact that the cursor is not in the same position in all windows when you move the mouse to the bottom right corner means that beyond any smidgen of a doubt, your game windows are not rendering the same resolution.
Another problem you're going to run into is that you've removed D3Prefs.txt Virtual File from your characters, so when you play solo your settings are going to affect your multiboxing settings. So... when you go changing your solo setting to 1600x900 and probably even a different windowed mode, it's going to break your multiboxing settings. So I would put those back, first of all. (Worst case, you could go to File, Clear and run the Quick Setup Wizard again...)
And then, here's all you should need to do:1. Launch your team with whatever settings you currently have (without removing D3Prefs.txt from virtualization...)
2. In the options screen, in every window, before you even have to log in, click Options and change the windowed mode to WINDOWED FULLSCREEN.
3. Close Diablo 3 so it saves the setting
4. Launch your team again.
At that point, assuming you have the latest builds of ISBoxer and Inner Space, the windows will each be in 1440x720 as specified in your Window Layout. And the cursor positions will, necessarily, be exactly the same...
The resolutions of all windows can be verified from any Inner Space Console window. You can right click IS and select Console, and it should pop up the main Inner Space window with a Console window in it. In that Console, enter in "relay all displayinfo" with no quotes, and each game instance will respond with its rendering resolution, window size, and whether full screen or windowed. If you continue to have problems, then a screenshot or copy/paste of that information might help.