I understand that you don't want to capture it because it will disappear from the grotto, but if you could capture the one that you think has the perfect IVs and upload it to pokecheck I would really appreciate it. I can't tell what's happening from what you've described, and being able to see the actual PID you are getting would be a very good indicator of whatever issue may be going on. You would need to RNG abuse the grotto to get a Minccino again, however.
Just as a final thing to check, you've verified that the gender of what you are capturing is actually female, correct? Because if I set gender to male in PPRNG, then frame 56 is Timid with 'Alert to sounds'. As to what is advancing your frame, however, I'm not sure.