PFR (like other De-combers) trys to restore original progressive material thats ended up being split over 2 frames.
It decides whether to pass a frame through untouched or whether the top field of the current frame should be matched instead with the bottom field of the previous frame.
The filter works on TFF material.
BUT on a transition from from processing state to the other, it does a simple interpolation of the bottom field from the top field so that any errors in making descisions are hopefully masked.
These interpolated frames only last for a few frames and are less visually disturbing than getting fields in the wrong temporal order when watching the output on a TV via an SVCD or DVD encoded disc.
So if your blended fields are bottom ones - then the blends will dissapear occasionally.
I recommend trying the filter with the diagnostic settings enabled to see what is happening.
I'd recommend PFR(ShowShift=16) and a quick read of the filters web page on what the colours all mean.
Let me know if any of this is confusing - its a very simple filter really.
Then - name the polish required
(inside joke from another place)
regards
Simon