You cannot use the same system number for two different systems. That is what is causing the problem. You could end up for example with 5.1.16 being OFF in one system and ON in the other system.
You can use the same number for 2 different systems. In fact, our state police are on 3 different systems, Conventional vhf, trunked 800mhz, and p25 trunked. I use the same system quick key for all 3 . So when I type 50.09, all 3 systems load up. And since I did not reuse any of the department quick keys, I am able to control what I want to hear pretty easily.
Our Fire is mostly conventional. But our counties Department of Fire, Rescue and Emergency Services is on 800mhz trunked. Same thing, fav list 50, system 1 turns on conv vhf and trunked system. In the vhf , the depts are numbered 1 thru 14. In the trunked system, its one talk group and its dept is 0. So those too can easily be controlled.
The issue I was having was for systems that did not share a system quick key.
I cleared user data and formatted the sd card via sdformatter, then wrote back to the radio. My scanner is good now.