Some shows have multiple logos.
When all logos are at the top or at the bottom of the screen there is no problem.
However, when the logo's are on diagonal sides of the screen Comskip will not accept the logo as valid.
A possible way to solve this is to set
subtitles=1
in your comskip.ini
This tells Comskip not to search for logos at the bottom part of the screen.
As a side effect it will speed up the logo search.