I had this yesterday, it could be 2 things, are you sure its the Timer0 fluctating, and your not hitting a second early? In RNG timefinder, look at the adjacent seeds and check the IV spreads, i kept hitting xx:55 seconds when i wanted 56 for instance.
Secondly, are you hitting your seed but just getting the wrong frame? I had been breeding solidly from a 53 frame start every time on the same seed, and then for this nido situation i kept getting it wrong because it started on 54 and not 53?!