Anecdotal, but some schools definitely care. My friend applied to one school but did not submit his secondary on his first cycle. He ended up reapplying, and when he emailed the dean of admissions at this particular school, the DOA asked him why he did not submit his secondary the first time. After a brief back and forth, this led to him receiving an II.
I don't know if it'll be like this elsewhere, and it shouldn't be a reason for you not to reapply, but be wary that it might matter.
Kevin W, MCAT Tutor
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