I don't think it's the profile or the ref frames (which BTW can be changed quite easily in the profile depending upon which encoder is being used). See this link for description of level/profiles, 4.0 and 4.1 doesn't matter unless your bitrate is very high. en.wikipedia.org/wiki/H.264/MPEG-4_AVC#Levels
Similarly references will only improve quality but take more time to encode.
Have you compared the frame rates? That would be one reason for a differnece in "smoothness" or stuttering.
Similarly references will only improve quality but take more time to encode.
Have you compared the frame rates? That would be one reason for a differnece in "smoothness" or stuttering.