Keyclone has always been a little weird with window swapping. It is the same for me sometimes it is real fast and other times it is slow. Sometime my windows stack when this happens this is what I do.

Say I hit F2 to and that window stacks instead of swaps.

I manually click in the F2 window and hit F1(main region for me) and this will reset the windows.

So my two monitors look like

Monitor 1: Whole monitor is main window and is F1
Monitor 2: Is four regions F2,F3,F4, and F5