Your example 1 is ambiguous in writing, but in speech the two possible interpretations have different intonations.
1a. You are not great because you know many things[pitch falls at end].
1b. You are not great because you know many things[pitch fails to fall].
The "not" in 1a goes with the sentence "You are great". The "not" in 1b goes with "because you know many things", and it is the first part of a contrastive construction in which "because you know many things" is compared with some other reason. This is why in 1b, the pitch fails to fall at the very end -- it is because the end of the sentence is only the first part of the contrastive construction, the rest of which is left unsaid.
So, in 1a, "you are great" is negated, but it is not negated in 1b, which implies that you are great. 1b means the same as your example 2.
In 1a, the "because" clause could be moved to the beginning, giving the unambiguous
1c Because you know many things, you are not great.