The only things that i'd point out (not that these are the cause of your problem).
There is no need to exclude the Clock from your zone. The time is added AFTER the image comparison is done.
You can enter EXACT values into the X/Y coordinate boxes (this means that you have more accuracy than the click/drag mouse option.
I would be inclined to create your irregular shape using many zones of regular RECTANGLES. This might be more of a hassle (your current single zone would become 4 zones, but it would simplify tracking down this issue (if it still exists once you use rectangles).