This was doing my head in too, for me it was caused because I was importing video and graphics with 1:1 aspect, and the sequence was 1:33 and interlaced. Once I created a new sequence with progressive fields and 1:1 ratio and selected all the old files and pasted them into the new sequence it worked fine, and all the pixelation was gone.
There is probably a way to change the settings on an existing sequence, but I couldn’t find it