It sounds like FM isn't refreshing the cursor when it has been activated as if it's still waiting on some further input that moving the mouse is providing. What about moving the cursor to a slightly different position after returning to FM, or going to an object on the layout to update its focus? I haven't had to do this before so I'm not certain it will work but worth a try.
Damon thanks for the reply.
I added a goto object step after applescript returns to FM, This got the closest to getting rid of the cursor anomoly, it happens a lot less
but it still happens. I'm going to try messing with the timming a bit.