The holes in sippy cups can be very small. Juice cannot have pulp or it clogs the holes. Milk and water should be fine, unless the holes are clogged from prior use. That was an issue I had with my son. It took me a minute to realize that's what it was.
Does he have reflux issues? I know very young children can get it. My aunt suffers from it and to control it her Dr told her not to drink while she is eating and that helped her ( some). Are you giving him the drink with food?
I've had many an ear infection w/out a high grade fever. My son gets fevers whenever he has had ear infections, so I think it must depend on the person.
Just some thoughts, sorry no real answers. Good luck!