I was just doing the same thing and had the same issue.
My settings are all on “best”. I’m using SD AJA NTSC 29.97 10 bit uncompressed (rendering in the same codec) all settings to best. I scale the video clip down) in this case to 25% of original size) then I render the sequence and it looks like it has scan lines in it – it barely looks any better than the preview version.
This really is odd because in scaling down one should not see the problem. Scaling up this would make sense, but not scaling down.
Anyone else seeing this? Does it affect SD only or is does it happen is HD. Is the codec wrong (10 bit uncompressed shouldn’t have a problem given the bandwidth). Where is Bob Zelin? 😉