This appears to be a reversion of prior buggy behavior, but upgraded batch sizes are not working if the tool is used from another tool.
e.g. If I select the Spice Grinder from my bag and use it, I can make Black Pepper in batches of 100. However, a recipe for Frying Pan requires Black Pepper and I go to it from the Frying Pan cooking menu, then I can only grind 50 Black Pepper at a time.
This was a bug that was fixed a while back but it appears to have reverted as of a few hours ago.