If I understand what you are saying, this is a pretty common occurrence with working with natural cultures. You do something one way for a long time, getting a specific result and then one day it starts doing something else each time. The reason is that by doing the same thing each time, you are slowly building up the bacteria that can exploit that circumstance.
In fact, it's a bit like Covid (I hope you don't mind me using that example). Here in Japan, things have been relatively stable since the beginning of the troubles. People wash their hands a lot, wear masks *all the time*, avoid talking in public, etc, etc. And so we were gliding along only getting a few hundred cases a day, on average. If the numbers went up, then we added some extra restrictions and the numbers went down. A few months ago, the delta variant showed up, but it made very little difference for a long time. Suddenly, in a period of a month, we went from between 10K and 20K active cases to 200K active cases. Adding extra restrictions don't seem to make any difference. What happened? We didn't change *anything*. Things were fine, before. Why aren't they fine now?
And that's exactly what happens. You're trucking along with your technique and everything seems totally fine. But in the background, you are getting a "house infection" that's very, very, very slowly building up. As soon as it gets to a critical size, it just explodes. Because your previous technique didn't deal with it earlier, it still doesn't deal with it now. It's the exponential growth that catches us out. It has the pattern of nothing, nothing, nothing, basically nothing, still basically nothing, OMFG WTH HAPPENED!!??
My advice is that before you store your whey, bring it up to 63 C to thermise it. Then store it in the fridge. If it's going sour in 24 hours in the fridge, then it's a cold loving bacteria, but I'm assuming that if your normal milk in the fridge isn't going off that you're picking it up from outside the fridge. Just keep changing your technique until it stops happening... and hope that you don't just breed up another super bug ;-)