Hi! I've been making yogurt weekly for about 5 years now, mostly from fresh Jersey/Brown Swiss milk but also from store bought Straus milk (pasteurized, non-homogenized) and I use New England Cheesemaking's Y5 Sweet Yogurt culture. Most of the time the yogurt turns out thick, without the whey separating out. I would not call it slimy, it is very thick and good. Even though the whey does not readily separate out in the jar, it will strain out using a Greek yogurt strainer or muslin or similar and it tastes great so I am very happy with it.
But I do remember a few times when it would separate out into a more fragile "curd" and whey. Most recently when this has happened, I sleuthed it out to be the variations in milk...different cows getting different feeds at different times, with widely variations in cream content. I don't think it was the culture as it's the same one I've been using for years, although I suppose it could be suspected since there have been different batches used. Anyway, I don't recall the separation happening with the Straus milk, but since I am now using it (Straus) again, I will report back if I ever get the separation with it.
You said you're using the same milk, but is it possible there have been changes to the company's processing methods that could be causing your yogurt changes?
Your post also brings back to mind an article I read awhile back in New England's blog about an experienced cheese maker suddenly having trouble making cheese. She made the same cheese every week for years (I can't remember what kind) when suddenly she was having aging failures. She first suspected her milk, but was able to rule that out. Finally she realized her daughter was doing a lot of baking with sourdough starters and such, and suspected yeast contamination from the air. I guess it is possible to have a healthy population of yeast in the air when you are doing a lot of frequent baking with yeast and starters. I can't remember if she then tried a batch of cheese in a different location, or if she thoroughly scrubbed her kitchen and didn't bake in it for awhile, but either way, her cheeses turned out to be successful after that. So it turned out to be yeast contamination after all. Since you said you are doing a lot of baking, I wonder if that could be the issue with your yogurt? I understand you are proofing in sealed containers, but the yeast could be getting into the milk while you are heating and cooling it?
If none of the above are the cause, I think you have quite a mystery on your hands! Let us know when you figure it out, and most importantly, don't give up!