Thank you for your response, Kris!
The original footage plays very smooth in both PP and AE, but it was shot handheld and therefore a bit shaky.
As for the square pixels, the H.264 HDTV 1080p 25 fps preset shows a Widescreen 16:9 pixel aspect ratio which I change to square pixels, this makes me wondering too, since the original footage and the sequence are all set to square pixels.
I just did an export from AE using Quicktime animation with quality set to 80%. No change, as soon as I export out of PrPro, I get stuttering playback during all those scenes.
What I am wondering, if I set the H.264 export to max. bitrate of 40Mbit/s, why is the PS3 showing bitrates of >100Mbit/s during the playback of those AE clips, where the stuttering occurs?
As for CS6, I want to change, but I think I will wait for CS7. I have not yet made up my mind if I want to join their cloud program.