Error 103 means comskip was not able to write an output file.
The time between the finishing of the recording and the writing of the final output file has indeed increased.
OK, cool. Thanks. I can live with it but just in case there might be a workaround, here's how MarkCommercials calls com skip (from the logs):
Sun Nov 18 21:00:18 2012 - Changing directory to /Volumes/iB/EyeTV Archive/The Good Wife - Here Comes the Judge.eyetvsched
Sun Nov 18 21:00:18 2012 - Running: "/opt/local/bin/wine" "/Library/Application Support/ETVComskip/comskip/comskip.exe" --ini="/Library/Application Support/ETVComskip/comskip/comskip.ini" "000000001659f452.mpg" > /Users/me/Library/Logs/ETVComskip/374994002_comskip.log 2>&1 --verbose=10
So it appears to just be targeting the current working directory, which again, get's renamed before comskip has finished.