This may seem like a silly question, but are you publishing your map service with the table used for the label?
Also, you may want to look on the portal side and make sure the label feature option is turned on when you add the service to a map; and check your visibility range for the labels. I'm working with almost the same environment and I'm able to see labels in my services that are based on joined information so it's probably something you'll be able to figure out eventually.