What type of hay are you feeding? As in pasture (clover dominant?) lucern (alfa alfa)? If your hay is high in protein that could be what is doing it. Is it very dark, glossy, bubbly? Can you smell ammonia in the dairy when you are milking? And is it your whole herd, or just your fresh/mid or late lactation cows that are particularly affected?
A few more details and I may be able to give you some pointers.