I had the same problem,when i reported this is how the conversation went

ME:I brought the keyclone software yesterday
set it up for dual mode
Problem: After few minutes in to the game mouse fails to interact with the interface of the alt window,alt window responds normally to keyboard.

My system runs Windows Xp- mouse works fine otherwise.

if u need more info i will try to describe in more detail
HELP:what os? are you using maximizer? can you still move your mouse over the window? do you have 'focus-follows-mouse' enabled under keyclone/setup/general?
ME: My OS is Windows XP- I am using the lastest version of Keyclone,
"NO" i cannot move the cursor over the alt window,it doesn't move beyond the edge of the window,it works fine on the rest of the screen(even fine on the Main window )
"YES" i use Maximizer with horizontal split
"yes" Focus-Folllow-Mouse is enabled in my setup
HELP:
ahhh. there is a situation where there is a known bug. it's a mix of wow and keyclone, and i am working on it to resolve it for the next release.

basically, when you click-drag in a wow window, blizzard hides the cursor and moves it outside and to the left. when you let up, for a moment, blizzard leaves the mouse hovering over the window to the left of the click-drag window. if you move your mouse quick enough, and have 'focus-follows-mouse' enabled in keyclone, keyclone will push focus to that window... and the mouse-up event never goes to the original window. as such, when you try to mouse into that window... it thinks the mouse button is still down and puts the cursor outside and to the left of that window.

you can correct it by quick-clicking into the window. you could also avoid the issue by not moving the mouse immediately upon letting up on the mouse-click. you could also disable the 'focus-follows-mouse' option in keyclone.

and yes, this has been discussed on the forums.