No, it wasn't the first time Logan had seen Jimmy without his wig. The first time he met the boy he'd looked a lot like he did now, only more scared and with less control over his ability. Jimmy, of course, was surprised, but Logan knew that the explaining was going to need to be done fast and they needed to leave before another sweep came through. He told Xavier this was going to be quick and he meant it.
"We're putting you in a safehouse," Logan said, "so pack your bag and we're leaving as soon as possible." That was all the explanation that Logan was going to give and he stood near the door, arms folded and watching Jimmy as if waiting for the boy to just get on with it already.
Not the wake up that he wanted, but you can't always get what you want.