I set the shortcut to run as admin but the problem is still there.
I run Vista home premium 32 and a Nvidia 8800 GT.

After further testing here is what I found. The focus follows mouse works if the monitors are set with monitor 2 to the right of monitor 1, it also works if monitor 2 is set to be below monitor 1. The focus follows mouse doesn't work if the monitors are configured with monitor 2 above monitor 1 or monitor 2 is set to be to the left of monitor 1.

Thanks for your help.