I just finished a job in PrPro CS6 on a Windows Machine and experienced some strange behavior while editing. First everything went normal, but the bigger the timeline got (in the end about 45 min), PrPro got slower and slower. In other words: realtime playback wasn't working sometimes, I had to stopp first till it loads into RAM, then start again. And scrubbing over the clips sometimes took hours to show a picture in the canvas.
It was shot on XDCAM and on a 5d, the workstation I used was brand new (ivy bridge i7, ssd, 32GB RAM, geforce gtx 680).
I set the scratch disc on C, which is my system drive, but it runs on a ssd
Couple of things I can think of here.
One is insufficient disks. Three really should be considered a minimum for any usable edit system:
C: Windows/Programs (and nothing else)
Second is the duration of the media itself. CS6 has a bug with some types of spanned media, like XDCAM. Longer clips (over 20 minutes) will exhibit a drastic slow down in performance. If this applies to you, the only solutions at this time are to use an earlier version of PP, or to convert the media to something else before you import it into PP.