First, since some of your game windows are smaller than 800x600 you'll need to use Windowed (Fullscreen) as per this post here (which you said you've already read).

Second, that post I just linked also mentions that Diablo III doesn't like resolutions which "are not close to its favorite Aspect Ratios." I see you're using two different aspect ratios in your Window Layout (2.0 and 2.2), both of which are... awkward. If you just enlarge Region 1 to 1600x720 then its aspect ratio will match that of the small ones; however, I'm not quite sure that a 2.2 aspect ratio is a good one. I would suggest to maybe choose a new layout, but that's quite a unique monitor you have in that it only has a max resolution of 1600x900; so, your choices are probably limited.

Third, as a handful of other posts in the ISBoxer D3 forum have mentioned, you can always just go into your Repeater Profile, change the Cursor Positioning Mode to "Scaled to Fit​", and hopefully everything will pretty much be fixed (although this isn't the best solution).