I've started double checking it, and it only seems to happen if I switch from my bigger buggy batteries to my 900mah chopper 3s stuff. I'm now just selecting the 3s battery twice and that keeps the current set right.
I bought this charger used, so I'm sure its out of warranty. Maybe this is why it was so cheap

Otherwise it seems to be a great charger; I just have to watch it when charging the small stuff