If you're using different in-game resolutions, there is not going to be any way for mouse broadcasting to perfectly line up. The game won't put things in the same place, it wont be the same size, it wont be the same aspect ratio. As you have discovered.
You CAN make it line up with some work. A while back Zorba showed me his EyeFinity configuration, where he wanted 1 window spread across all 3 of his monitors, and his others just on the center monitor. To get it working for him, I added a "Cursor positioning mode: From center" option in the Repeater Profile, and then he made sure all of his UI stuff in the game lined up perfectly on his center monitor. So it might technically be possible for you to set it up to all line up. That is definitely NOT the easiest way to go about it though
More generally, if you want mouse broadcasting to work correctly, you want to pick a style of Window Layout that allows all of the windows to be the same resolution. That doesn't mean "the same window size", just "the same resolution". Of course, if you match the resolution at the different window sizes, it's going to look stretched one way or another because the resolution will be scaled to the size of the window. Mostly, this means having the "Instant Swapping" option enabled in your Window Layout, which synchronizes the resolutions of the game windows.
Finally, one last suggestion. For multi-monitor users in particular, I usually try to recommend making better use of the screen space by picking the important parts of the game windows to display on the second monitor, instead of showing the entire game window(s) on it. This is done by using Video FX
-- you can take whatever piece of the game you need, put it where you need it, and interact with it there as if that part of the game was actually right there.
* How to add a blank window for your video feeds!
(the blank window is called dxNothing)
* Common modifications: Video FX alternative to Window Layouts