I had the same problem and this what was my issue and solution. Don't know if it affects the issue, but I am using DisplayFusion to administer my backgrounds across both monitors.
Anyway, when I set the background (in Dexpot) for each desktop, Dexpot reset the monitor configuration one atop the other. This is where you get the mouse tracking from bottom of screen 'A' to top of screen 'B'.
Fix: I went to my native desktop configuration 'Right click on the screen and pick your configuration manager' and I reset the desktops to being side by side. In my case I just drag n drop from the 'top to bottom' to a 'side by side'.

Note that each time you set the background in Dexpot it resets your monitors to be stacked atop each other.

Please enable the Dexpot log file, reproduce the problem and then send me the log.

Hi,

I have a setup with 3 desktops on a 2 monitor system. Switching is enabled for the main monitor.

When I'm on desktop 1 or 3, if I move my mouse to the top of the screen (very easy when trying to click on tabs in my browser), if the mouse touches the top of the screen, Dexpot switches to desktop 2.

I do not have any mouse switching enabled in Preferences. This is new behaviour in the latest release.

Please help!
Adrian