She wasn't just humoring me. Her eyes really understood my feelings and showed sympathy.
Literal
Just, tune [object-を] matching [progressive-ているんじゃない]. Really, my [genitive-の] feelings [object-を] understanding sympathizing eyes was.
Two-sentence introspective narrative. 調子を合わせる ('to go along with, humor, pretend to agree,' literally 'to match the tone') is a key idiom. The negation んじゃない here is the strong denial form ('it's not that X'). The second sentence ends with the verbless predicate 目だった ('it was [the kind of] eyes'), with a relative clause modifying 目. A nice demonstration of Japanese's freedom in turning verb phrases into nominal predicates.