yes, I've got it running now on my system ...
take a look at Rung 001 in your Initialize routine (Ladder 3) ... notice that you're Latching On the "Going Up Flag" B3:0/1 every time the system goes into the Run mode ... is that what you REALLY want to do? ...
maybe it is - maybe it's not - but before you answer, take a look at Rung 001 in Ladder Routine #8 ... notice what TRUE conditions will be present as soon as you put the processor in the Run mode ...
suggestion: as a debugging experiment, just temporarily CUT out the Latch for bit B3:0/1 in Ladder File #3 ... see if that gets you any closer to where you need to be ...
if I understand your original problem, then maybe this will help ... if it doesn't, post again and tell us where it hurts ...