Forget the "directions" and quadruple your rennet next time. Every type and batch of rennet varies. Search on flocculation.
Thanks Sailor Con Queso, I think you are right, I tried to make a mozzarella the other night and had the same problem.
So it has happened more than once , I've had that happen too , sometimes it's just the milk and no matter how much rennet you use , it just doesn't set properly.
I have found that if the curd breaks up very small and won't separate from the whey , add VERY hot water and wash the curd , even if you aren't doing a washed curd cheese , it will help set the curd and separate it from the whey.
Yes , it will change the outcome of the cheese , it won't be the same cheese you set out too make , but it will salvage the batch , and in my experience , it has produce a very edible cheese every time , in fact some were downright delicious.
And being as you started with a thermo anyway , the hot wash won't hurt it.
I do this for a worst case scenario , when you think all is lost.