...are you using from mediaportal client or TVServer pc.
To see whats going on (whats flashing up in that command window), try adding "> C:\out.txt " to the end of your comskip arguments, this (in theory) should output whatever shows up in the command window to the file C:\out.txt - might have some helpful info in there!
If you go to the MCE Buddy website, there is a comskip.ini pack you can download which is updated for each country, so you need to edit your country name to the default comskip.ini that exists in your comskip folder, that should give you better individual results.