Wierd problem with draft vent of water heater.
 

"Mikepier" wrote
The only thing I can think of is that it was very humid outside last
night and the air was still, possibly causing no updraft.
I rechecked about an hour later, and the draft was good. What could
cause this?

Do you have an exhaust fan? Attic or whole house fan drawing lots of air?
They can cause back drafts if there is not enough window/door openings to
allow lots of air in.