That's odd. SP2 will at least do the conversion to YUY2 for you if you didn't (albeit not as well as avisynth can). You'd think they wouldn't remove that feature.
Btw, did you also remember to do a BT.709 to BT.601 conversion? I always forget that when my source is HD.
I've been watching this thread only because I didn't even know there WAS an SP3. I had no idea they were still developing CCE. Everything sort of died with 2.7 for the longest time.