This is somewhere between a feature suggestion and a bug, so I thought I'd just post it as a suggestion.
It appears comskip is crashing if the hard drive is full where it attempts to open and write files. I am using comskip with DirMon and when DirMon spawns comskip, comskip will immediately crash if the drive is full--every time that DirMon attempts to respawn it. This should be 100% reproducible, but I can provide logs or data if needed.
I'm running comskip 0.79.15 (will d/l .16 shortly).
Thanks for all your work on comskip. It is absolutely awesome and has revolutionized my TV watching!