https://github.com/ps3mediaserver/ps3me ... er/pull/98
It is the problem of TV itself. When file is streamed as is (AVI), TV shows correct AR but when file is remuxed or transcoded (mkv-->ts/mpg), TV will expand the picture to full screen also in case black bars are removed.
It can be fixed by transcoding only.
In PMS there is a bug which is described in link that AR fix is ignored. You can try using this fix by adding this line to custom params in Gui:
Older MEncoder versions used softskip at the beginning with :1: part. New versions don't like it so we should use softskip at the end and :0: part. Without it subs are not rendered correctly.