Curt,
That is a problem IMHO with the scanner design. I live with it and avoid it by making sure that when I edit a system (on the PC) and then upload just that system, I first delete the current copy on the radio.
It seems like a simple "duh" to me, that you should not be able to have identically named systems in the radio at the same time, but that is just me. At the minimum the radio ought to announce that there is a system with that name in it before allowing you to upload it. It is one of the few things that are a minor irritation with this radio.