in earlier versions of After Effects it was possible to set the quality of the Pixel Aspect Ratio Correction to "high" resulting in a very nice and clean preview. In CS5 this seems to be not possible anymore, because the standard and already set option in CS5 is "high". Anyway - the PAR correction looks very bad in CS5, giving me choppy vertical lines. Is there any chance to get a clean result like in CS4?
Prefs file --> Viewer Odd Zoom Quality
Open GL may not handle PAR Correction well. Try turning it off.
The Zoom Quality preference also affects pixel aspect ratio correction for previews.
Keep in mind that the pixel aspect ratio correction setting in viewer panels is just a preview setting; it has no effect on final output.