With mplayer/mencoder one can remove the station logo as detected by comskip
Use the following command line
"C:\My Programs\mplayer\mplayer.exe" -vf delogo=1114:624:103:37:2 %1
where
-vf delogo=X:Y:W:H:T
is the logo removal filter
Where X:Y is the top left logo position counted from the top left corner
and W:H is the width:height in pixes
T is the blurring border, setting T to -1 displays a green bounding box to enable tuning of the logo blurring position.
I may in the future be able to have the command line parameters generated by comskip but the .logo.txt file already contains the relevant information.
The first 4 lines of the .logo.txt file where
logoMinX=1114
logoMaxX=1217
logoMinY=624
logoMaxY=657