Ok see now what you are doing however not sure I can get the problem.
I used your xml and set to tool 2, shut Mach down and restarted and the Tool DRO was 2, User DRO 2000 was 2 and in the Brain it still said 2 on the mod output so not sure why it would send a call for tool 1 to your PLC. I am wondering if it may be your ladder that is doing this?
Hood