Anusien, you are correct that "Not A." could not be concluded from that. The statement "If B then A" is what is called a material conditional, and it is true for all truth value assignments except those under which B is true and A is false. So to say that "If B then A" means that A ONLY happens in the case of B would be incorrect, since the antecedent (B) could be false and the consequent (A) true and the molecular sentence (If B then A) would still be true. You are thinking of the statement "A if and only if B," which is a material biconditional and entails both "If B then A" and "If A then B."
Limbo's description actually is a material biconditional, and it is actually the best description of the matter. Seedborn Muse could be rendered as "Untap all permanents you control if and only if it is the beginning of the untap step." Stasis removes the untap step, so the second atomic sentence (It is the beginning of the untap step.) will always be false. Since, in a material biconditional, both atomic sentences must have the same truth value, it will always be false that your permanents are untapped.
Of course, none of this is mathematics. It's sentential logic, which is taught in the philosophy department at most schools.
Thank you for overcomplicating the first week of logic. By the way, I've never heard it referred to as atomic sequences or material conditionals; are there immaterial conditionals (and yes I have taken courses on this)? Incidentally, it never made sense to me why some schools teach this stuff in philosophy. I took a summer class in Logic under Philosophy, and then took it at college under the heading of Discrete Mathematics. The math aspect makes more sense, because it has direct applications to set theory.