Today I solved my own problem. kind of.
It seems that Compressor would not output the standard ProRess setting at 16:9 so I set the frame size to 1600 by 900 and the pixel aspect to square. Not only did this solve my apsect problem but also a smooth slow mo issue.
I had already changed the frame rate from 25 to 50. (I am in PAL territory) Next I conformed the footage back to 25 frame in Cinema tools and it plays back slow and nice and smooth.
I had read about this smooth slow mo technique on a another thread but was always unable to do it. The results are great!