The problem with some YUV formats is the chroma subsampling. The subsampling happens when converting from RGB to the YUV format, so
before the actual encoding.
Subsampling
may blend the (color) information of neighboring lines together, lines that belong to different fields and hence shouldn't be mixed together!
See this for more info:
http://en.wikipedia.org/wiki/Chroma_...ems_and_ratios
(I think 4:1:1, 4:2:2 or 4:4:4 would be okay for interlaced, but 4:2:0 wouldn't. Guess that's the YV12 -vs- YUY2 difference mentioned by squid_80)