In the Meedio forums, there was a user having an issue with the commercial skip....and to make a long story short, I think there is a bug in ShowAnalyzer that is causing the frame numbers in the chapters.xml file to be divided by 10 before being writen to the file. I was running v0.6.0.158 previously without problems, but after upgrading to the current v0.6.0.209 I've got the same problem.
The times in the chapters.xml file are correct, but the frame numbers are way off. By looking at a correct cut file from the older .6 version, it looked like the frame numbers were 1/10th of what they should have been...and adding a zero to the end of the frame numbers corrects the commercial skipping for the cut file created with the newer .6 version.
For reference, the thread on this subject in the Meedio forums is at:
http://www.meedio.com/forum/about28202.html
If you need a log file or more info, let me know.
Thanks,
Jason