I think I've also been experiencing this issue, although I thought I had narrowed it down to b-frames, rather than main vs. high profile (main profile H.264 is probably decoded using Apple's H.264 decoder rather than Perian's, which would explain why the problem doesn't show up when encoding main profile).
IIRC, I only noticed that with files encoded using MPEG Streamclip and x264Endoder (i.e. high profile H.264 - with b-frames - encoded using QuickTime 7 and x264Encoder doesn't seem to trigger the issue).
Mr VacBob wrote:I wonder if it's a regression in Perian or in ffmpeg?
Do you need additional information?