While trying to make cheese I tried to insert a bucket of milk into a Cheese Vat but nothing happened. After some trouble shooting I found that items linked to Food Funk cannot be used in Growthcraft machines. So far i've tested that items linked to Food Funk can not be used in the Cheese Vat or Pancheon and I assume this is the same for all other machines and Food Funk items. I'm not entirely sure why technical wise but I guess it's something to do with not recognizing the item.

Sorry in advance if this has already been mentioned.

Quick update:
After some further testing it is just putting liquids linked to Food Funk in the Cheese Vat or Pancheon that causes the problem.

That is correct, we do not have compatibility with Food Funk. We are currently working on the port to 1.15 and 1.16+ we can put this on the list, but will not be adding new features to 1.12 until that port is done.