sure there is. First thing that pops to mind is to have a variable called "timer_pause_time" or something. When you load the first layout, you check if it is 0. If it is, it's the first time you load it, and you're not returning from the "sub"layout I shall call it. If it's not, that means that you've returned from the sublayout and you start the timer from that time instead of the initially intended time. When you go to the sublayout, just set the timer_pause_time variable.
sounds good? Hope it helps