Comskip running sporadically about etv-comskip HOT 6 CLOSED

I think I discovered why one of the two recordings failed to have comskip run 
on it.
 I tried to run MarkCommercials.py [EyeTV id] and there was no output.  I opened the
mpeg file with MPEG Streamclip, and it indicated there were two Video PIDs!  I 
tried
to export from EyeTV to Program Stream, and EyeTV indicated that there was a 
channel
change in the file and that it might not export fully!  Huh?  This was a 
scheduled
recording.  Next, I opened the EyeTV editor and chopped the first and last two
minutes of the recording.    I ran MarkCommercials.py on the file again, and now
there's normal looking output.

What would cause two Video PIDs to be created in an EyeTV recording?  aspect 
ratio
change by the station (from SD to HD)?

As for the other recording, if I run MarkCommercials.py on it it appears to have
normal output, so I don't know why comskip didn't run on it.

[deleted comment]

You can select a PID to process in Comskip
If not specified Comskip will process the PID with initial the highest video 
bitrate
(for SH/HD multicast)
If there are multiple PID's because of a program switch you are out of luck.

Forgive me for my ignorance.  I have just started using Comskip, but it seems 
that no new programs are getting 
marked automatically.  I have launched FileWatcher.  This worked before, but 
now the only way I can get my new 
recordings marked is to run FileWatcher on my entire EyeTV Archive (the command 
in the Read Me).  I'm running 
EyeTV 3.0.1 and Comskip rc6 under Mac OS X 10.5.2.

Issue 18 has been merged into this issue.

merged into bug 27 and fixed