in the early days of shippuden...when they were tailing deidara after he took garra, he told naruto that it was his new weapon...so even thought we seen that he got it same time as obito, then that means he either never was desperate enough to use it or didnt know how to use it yet
When he awakened it as a teen he fainted and forgot, so he didn't have it until part 2, he awaken it again. It wasn't explained how he awaken it in part two he just did.
it requires a lot of chakra and a good uchiha body, since kakashi hasn't an uchiha body and not a lot of chakra, it's hard for him to use it, he knew that he had it, but he just had to learn how to use it.. it's very difficult for him
i don't think that even Kishi knew about MS back then, but let's say Kakashi didnt face opponents strong enough to waste MS abilities... i mean... he kinda faints every time...
He may not have known about it, not have had enough chakra, or just didn't know how to use it. You could see against Deidera it took him long just to keep his hands clamped and mold chakra, while now he does it without hand signs.