You should always call the doctor if your baby has an unidentified rash. The sooner he's treated, the sooner he'll be more comfortable.
The doctor will take a look at the rash and possibly do a painless test that involves scraping off a small sample of skin and looking at it under a microscope. Scabies mites and their eggs are visible when magnified. Mites can be easy to miss, though, because there are usually only ten or fewer on an infected person.