Hi John,
I have placed a new RW_Tools.exe in a zip file at
http://www.rstools.info/Public/RW_Tools.zipThe problem seems to be that for some reason I had the option 'Don't change numbers when swapping stock' in both the main screen 'Options' menu and on the Scenario editor screen and one was overriding the other.
New version only has it on the Scenario Editor screen, so make sure it is not ticked while using the option in this case.
I have tested it and the problem is that on the GP9 the numbers are only available as 3 digit items. If you are swapping from a 4 digit loco like the SD40 then nothing shows if you ask it to maintain the original numbers. However if you allow it to change the numbers, then RW_Tools selects a number at random from the GP9's DCSV file which lists valid numbers.
As you have already changed the locos, probably the easiest way to fix it is to swap all of the existing GP9s for BNSF GP9s and then swap again back to the Milwaukee ones and that should fix all of the numbers.
One thing you should note though is that if the Scenario requires the original loco numbers (Often needed when picking up wagons), then you can swap the locos using the original numbers, they are saved in the Scenario.bin file, but they will NOT appear on the locos.
Please let me know if this works OK and I will upload the file to my normal site.
Mike