Could be Apple handling of gamma; there have been some issues and changes with this.
How are you monitoring the flvs - on your Snow Leopard machine? Have you checked them on other machines?
Flash / the web is largely gamma-unaware, assuming gamma 2.2. Apple pre Snow Leopard used a default gamma 1.8 (better for print was the reasoning, apparently) though now has default gamma 2.2, like the web, most windows boxes, TVs.
I have the same issue. Wish someone could explain it, it appears to be directly related to the prores codec. If I transcode to a H.264 then compress to flv, the problem disappears. Weird. So there's a solution (albeit a rather annoying one) that has worked for me. I must also add that it is definitely not a gamma issue, the overall brightness is down on my renders. Anyone?