I am not quite sure what the problem is. Do you mean that you don't have squad highlight turned on anymore, or that when you turn it on, you don't see orange icons?
I think Cntrl-S toggles squad highlight? Hopefully somebody will confirm that for me. Try CNTRL-S and you will see a message in the radia bar confirming squad highlight on or off. Once you set it, AH will remember your setting for next time.