It sounds like it's applying an offset to run inside the rectangle instead of outside it. If your hand-written Gcode works, but the Fusion-generated code doesn't, it's not likely to be a Mach4 problem; I'd look at the G-codes Fusion is inserting at the top of your program (like that G54).. Eliminate any that you wouldn't put in on purpose, and see what it does when run. There's probably a setting in Fusion that tells the tool where the tool should be in relationship to that rectangle; and since it's set incorrectly, it's deducting the radius twice instead of once.