Setup:

Dual LCD 1680x1050

Display 1: Full screen used
Display 2: 4x4 grid

Problem:

Keyclone resets the window positions upon changing settings.

Steps to reproduce:

1. Launch 3 sessions. Display 1 at full screen, display 2 using a the bottom half of the screen for 2 isntances.

Code:
+------------+------------+
|        	|        	|
|   FREE 	|	FREE	|
|        	|        	|
+------------+------------+
|        	|        	|
|  SCREEN	|  SCREEN	|
|        	|        	|
+------------+------------+

2. Enter the setup for Keyclone. Go to the do not pass entry and add a key.

3. Press Ok.

At this point the windows will reset. In my case, the lower right window went to the upper left quadrant.

Note: Couldn't get the screen layout to be exact, but I think you get the point from the drawing.