You may be an English teacher, but clearly not a linguist!

I am a linguist, and I can tell you: you are correct, correct, and incorrect.

It's not a punctuation difference... correct.

It's a linguistic (or linguistical, if you're a brit) difference.... correct.

But ALL differences to do with language are LINGUISTIC, whether its orthography (punctuation), syntactic, morphological, lexical, or what have you.

So even if it WAS a punctuation difference, it would still be a linguistic difference, so..... (incorrect).

In this case, it is a morphological/lexical/grammatical difference.

Morphological difference:

Your (possessive pronoun - one morpheme) vs. you're (contraction of 'you are' - two morphemes, second one being a conjugation of the verb (to be)).

Lexical difference:

Your = possessive pronoun (2nd person singular) - indicates the object is possessed by the person represented by the pronoun

vs. you're = pronoun (2nd person singular) + verb (to be) - indicates that the person represented by the pronoun is (something).

Grammar difference:

The former is a word, and the latter is a phrase.

For my money, the better slogan would have been :

"Grammar matters" because this is essentially a grammatical difference not a punctuation (orthographic) one.