Right before the opening credits, Colonel Sheppard is captured by a recurring villain named Kolya. Kolya bends over to taunt Sheppard and says, "It's good to see you again, Colonel."

Remember that Kolya is a renegade working for no one but himself. Unless he has an amazing spy network that works for him (which, although he probably has a few spies, he can't have that many), there is no way that Kolya could have known about Sheppard's promotion from Major to Lieutenant Colonel since the last time he saw our hero was long before that time.