I've double checked all of this just now again. In the same project if I just drop the main source clip in a comp and render it, comes out fine. It's just this one comp in the project with the issue. I'm on a MacBook Pro Retina and no udpdates have been done recently.
Also I just did another shot for the client, same workflow and it worked fine. I'm wondering if adding shape layers to the comp is the issue? Maybe they cannot interpolate?
Shape layers are definitely not the culprit. If at all, this is probably a problem caused by multiple settings and effects. also it could simply be an issue with a temporal effect you use - anything from time stretch to Timewarp. you may simply have used unfavorable values there that quantize the interpolated output to the same field, which you do not see while working in AE since it doesn't do fields in the comp.