I'm having trouble with the timer, too. In 2k3 there seemed to be a lot more functionality with the timers, now in VXA I'm stumped.
I'm trying to set a timer to run for 3min continually, during battles and outside, then to have an auto-start activate when it's over. In 2k3 there were options to have the timer appear or be invisible, have the timer only count outside battles or both and to start/stop.
Now in VXA there's only start/stop, and it appears onscreen when I'd rather it didn't, it doesn't count down on the field and will only count in battles, and it resets after each combat ends.
Any clues how to resolve this to my desired effect?