My guess is ..the source footage does not match the sequence settings.
What are the properties of the clips from AE?
What are the Sequence settings?
with Match Sequence Settings.
Don't use that. Set your export settings properly and manually.
Shooternz: I wondered this.... but I dragged the clip onto the new sequence link so it'd make one the right size.
So the clip is 832 x 468 (1.0), and the sequence is exactly the same.
Jim: It was always an easy way to get a Master, which I then convert to the various formats with media encoder.
Worked fine in 5.0. Ok, I can work out some settings, but Adobe are supposed to be making my life easier with each upgrade, I hope... this seems like another step back.
If you want a Master for later transcoding, you definitely need to set things manually. You'll want to use a lossless codec, something like UT or Lagarith in an AVI container.