2 salt goes in the cheese vat just fine, but it won't accept a yellow dye afterwards.

I just tested it and it works fine. Which version are you running?

Is it vanilla yellow dye?

4.1.0

And just to confirm .....

1. 5 Buckets of Milk + Bottle of Rennet + Starter Culture, hit it with a wooden sword.
2. Waiting for it to turn colors
3. Remove the whey
4. Add the two salt + yellow dye

Yep. I used the same mix to make gouda after removing the salt.

Well, not sure that is going on then. I cannot reproduce the issue and Cheese doesn't use the config recipes.

Looks like we didnt confirm your bug ...

Sounds like the config recipes are out of sync. Delete your config/growthcraft directory and if you are still having issues, let us know. We still cannot duplicate the issue.