1) It only happens when I use the second window layout. With the windows positioned anywhere across the dual monitors display. It occurs also when I use just a single monitor (both flat screen and laptop screen).
2) I am unsure how I set both mine to the same resolution. I feel like I have done it before though (so that my mouse didn't collide with anything moving from flat screen to laptop screen.
New build available, please report if it doesn't work on your linux distro.
If you're experiencing visual artifacts on windows, try setting "Disable desktop composition" in the Compatibility tab of the radiant.exe file properties.