Yep, possible, in the form of acid buildup. The thing about pH is that it is an instant measure. It is a relative measure of the state of acid, and tells you little about how much of that acid has been absorbed. Casein bonds (the calcium phosphate) "absorb" acid and break apart. When they do that, the casein micelles don't bond together well, and the submicelles break down a little, too.
So you may start with a pH of 6.5 or 6.4, and not all milk with that pH is the same. In your case, the heat shouldn't do too much damage because it's low, but what you're doing is preripening the milk, then killing bacteria, then ripening it again. Also, by keeping it at that temp, the bacteria multiply, and more will survive pasteurization by the sheer numbers of it.
This is why I keep saying pH is a relative measure. Of course, draining at 6.0 and 6.3 are different in any case, but milk is a complicated thing.
When curds don't bond well, it's usually the acid, sometimes case hardening. In your case, try to add less culture and drain a little earlier.