Don't we have to be expert researchers to try and figure out our complex Yorkies and their ways, LOL!
Could be that kibble at night is too hard for him to digest? Perhaps you have some further experiments to really pin it all down?
My dog had pancreatitis once and the vet said I should feed him the Prescription diet to try and prevent it again. So far so good. He loves the kibble, but I give him some of the canned if his tum gets upset. Although the ingredients aren't what I would normally feed, this stuff sure works and keeps them well.
Good luck and keep trying