If you're control is brand new, you can perform a flash rom initialize from the boot screen to clean up the rom module. It sounds like you've check and made sure the modules are in the right location.
It also matters on how you enter the boot screen. You must go thru the maintenance mode (hold the right arrow soft key count 5 soft keys over and hold the very next soft key. Basically you have 5 softkeys between your thumb and pinky).
This will allow you to access the software and upload.
You can also do a system data check from the boot and look at individual software files. All fanuc software will be legible (ex. BEB1 000E 020). Builder software will be unreadable.
Finally, if you are copying from another machine, right down EXACTLY how it is listed in the other machine on the system data check screen (in the boot) and put it in this one exactly the same way.
This only works on a Model B or Model C. No way to do it on a Model A (no memory card slot).
Hope this helps. Be patient and take your time.