I get this exact same issue with most clips in Adobe Media Encoder CS5. Most clips are Avid DNxHD but it also does it with other codecs. It is the “Render At Maximum Depth” tick box that affects it, If i have that box ticked, then i get issues. I can drasticly reduce (but not get rid of) the issues by using a colour legaliser effect on my sequence before exporting. There must be something machine specific though because i can use the same Adobe Media Encoder preset on another machine without issue.