I switched from Keyclone to IS Boxer, so haven't used Keyclone in about a month or so.

However, prior to that time, I did not experience freezing in Keyclone until I upgraded my system.
I still get the random freezing with IS Boxer too, so its not the boxing program per se.

In my case, one of the windows (usually a slave, but sometimes the hot/master toon) will freeze.
I can switch to another window by clicking on it, or using my PiP hotkey to switch.
But cannot switch back to the frozen window.
It won't close in task manager, or Alt F4 or right clicking on the task bar.
And once I close all of the wow windows, the keyboard and mouse stop working entirely.
Can restart keyclone or IS but it doesn't replace the locked window.
The toon eventually goes afk and logs out, but the window is still frozen.
The only solution to unfreeze it, is to reset my system or power off.

I'm not sure if that is the same issue you're having.
Prior to upgrading to the i7, I did not have this at all.