Just my 2 cents…
R_Strev in the Live Hub forum was having stuttering .mkvs with VC-1 codec
http://community.wdc.com/t5/WD-TV-Live-Hub-General/Judder-on-just-one-mkv/m-p/557955#M23772
he/she forced the resolution setting to 1080i which seemed to resolve the problem from him/her
personally though, a bit of a pain to do that … also, personally i’ve never had any problems with mkv/vc-1