I had this issue as well, some browsing of the window layout options showed that it didn't default to region swapping when mouse swapping and such. I just had to click a couple options and BOOM all better!

the only problem i've got now is(and i've not checked into fixing it myself yet) that when you window swap your mouse used to follow the new screen , which made it pretty awesome to use dual screens for. Now when i mouse over to my left monitor and mouse swap to an alts screen, the mouse doesnt come back over to the main monitor with it... is this intended lax?