I just wanted to chime in and say that I absolutely don't think that is the case! I was accepted to UMass for fiction earlier this week (still reeling) and had included a flash piece. When I was admitted the person I spoke to quoted a sentence from my flash piece as something that they liked--so, if anything, the flash I included was super important in my portfolio. I'm sure the same is true for you!
I am late to the party here, but looking forward (maybe?) to this admissions cycle. I applied to Brown, Columbia, Cornell, NYU, UC Irvine, Iowa, UMass Amherst, Michigan, Texas (Michener), UVA and Florida.
Best of luck to all!