The first few batches I bake look good and have a nice thickness to them. The last few batches are thinner. Why would that happen? For reference, I use the Nestle Tollhouse Chocolate Chip recipe.
The fat in your dough started to soften/melt - especially if you have a hot oven running in the kitchen. Keep your dough cold in the fridge between batches.
See this question for more details on the issue in general, but for your situation, keep it cold between batches. You seem to have started correctly, which is good - you just have to keep it going right.
The suggestion by rfusca to keep your dough in the fridge between batches is good. Also consider the pans, though. You should let them cool down before scooping dough onto them. I have three cookie sheets, so I can have one in the oven, one cooling down, and one that I'm loading up with the next batch of cookies.
Similar to Adam's pan rotation method is to use sheets of parchment paper:
- lay out your cookies on the parchment paper on the counter
- transfer the paper to the pans immediately before cooking
It's not quite as good as letting the pan cool down fully, but the cookies won't have as much time on the warm pan to start spreading before they rise & set. It's also useful for when you're doing large batches, as you can get all of the cookies out of the pan in seconds, so they won't continue to cook on the hot pan