This issue has been SOLVED. In fact there were two causes of the problem of judder/stutter in full HD movies.
I noticed some judder/stutter in full HD movies. The problem was quite irregular, movies could run smooth for seconds on end and then suddenly there was a short stutter as if one or more frames were skipped from playback. This was visible when the camera was panning but also during action scenes.
I noticed with the O command that in full HD movies indeed some frames were skipped, about 100 in a complete movie, so not a lot. The number of frames lost could not explain what I saw on the screen. I had a feeling there was another issue. In fact I noticed that also SD material did not play as fluently as on a normal DVD player.
It seems my Geforce 9600GS was not enough to display high bitrate H264 encoded material without frame dropping. I have put in a Geforce 520 GT. Afterwards the frame dropping was gone.
I still noticed some additional judder/stutter though. It was frustrating the hell out of me but I could not put my finger on it. My PC though 4 years old is a regular power plant so power could not be the problem.
I found out that the cause of the remaining problem was this:
I use Windows in a lower resolution as my XBMC. The reason is simple: even though my TV screen is large (46") full HD resolution is too high to be working in Windows. I use Windows to play browser games and do some occasional video editing. When in XBMC I want full HD of course.
I noticed that XBMC does not play video well when resolution set in XBMC is higher than the settings in Windows. When I first switch to full HD before starting XBMC the problem is gone!
Finally I can start watching movies and enjoy the content instead of worrying about the playback!