Iv'e always had success using this set up for long timing periods (these presets for 15 second test):
001 902 901
-| |--|\|--------(RTO)-
PR 0050
901 902
-| |-------------(CTU)-
PR 0003
901 901
-| |-------------(RST)-
RE 0000
002 902
-| |-------------(RST)-
RE 0000
Never had the need to program the CTU to reset itself, always used some other sequence or discrete to do this, and after trying it out it out in the above rung order, didn't work for me either. I found if you use 902 to energize an output like 011, use 011 bit to trigger the 902 RST but move the RST rung to the beginning of this ladder, it will repeat itself like you want and you can visibly verify this watching 011 pulse every 15 seconds on the front of the unit. Yes, it is a pain not being able to watch the increment with PCIS, but I believe it may be possible with the hand-held programmer although I don't have one to try out. Hope this helps.