i have no idea... i would doubt the ui portion of the comskip (ie comskip playback for the default ui) would impact playback in anyway (it doesn't effect it on my setup). What could effect playback is the commercial detection process. That is a fairly resource intensive process (especially hdpvr recordings) and if your server is not up to it it could get bogged down between the transcoding and comskipping. My q6600 pegs one core when transcoding and one core when comskipping hdpvr recording (hdhr recordings are much less resource intensive).
