I have been noticing that when I convert recordings with the myth2ipod feature it appears to use the detected commercials. If I go into the recording and manually fix the cutlist and save it. I verify that the changes have been saved. Run the "encode to ipod" job option. It still pulls the wrong cuts.

I even tried creating my own job option using the encode to ipod setting minus the "cut" switch. Same result it uses the detected cut list

Sorry if this does not make sense, also I have no idea where to start looking for the problem.

Sounds like a bug in myth2ipod. There are several types of marks in the recordedmarkup table, and for some reason it's using the start/end ones from commercial flagging. Vague recollection says that the discussions around it included a desire for completely unattended operations, even though as you've discovered, that works better in theory than in practice.

My guess is that the author assumed that they could trust the commercial flagging and only searched for that type of mark. It would have probably been wiser to search for user defined cut points first and if none were found maybe fall back on the ones from commercial flagging. Better still to make it a config option.

As a work around you can run the lossless (*) transcoding first then run myth2ipod on the results.

(*) It's not completely lossless since it loses CC information from the recordings...

It's been a while since I messed with it, but as I recall the myth2ipod script's use of the -cut option wasn't exactly intuitive. If you run it with no -cut option, it actually uses your saved cut list (if there is one). if you run it with the -cut option, it generates a new cut-list on the fly using the commercial marking (obliterating your saved cut-list).

I typically edit and save a cut-list, and then run the myth2ipod script with no -cut option.

This thread might be helpful for you:
http://mysettopbox.tv/phpBB2/viewtopic.php?t=17151

I detailed some modifications I made in the myt2xvid3 script that is packaged with R5F27. It worked fine for quite a while, but after something bizarre (and still unexplained) happened to my mythbox, it would give inexplicable errors. So I have actually started using the script posted by brfransen here:
http://mysettopbox.tv/phpBB2/viewtopic.php?t=18169

I believe this uses only your cutlist and not the flagged commercials. So I have actually made a user job to create a cutlist and I have that enabled to run after every recording.

Hope this helps!

Thanks for the suggestions, the solution that appears to be working best for me is to Transcode the recording before Encoding for ipod.

This does lead me to another question: How do I go back and "fix" the ones that were done earlier? What I mean is I have a recording that was transcoded to Ipod but used the autogen cut list. No I want to delete that recording and transode it again to get the correct cutlist.

I have tried deleting everything in the ipodfeed folder, but when I re-run the encode for ipod it is still "off" by off I mean the transoded version is 43min long and the encode for ipod is 21min long.

This is only for jobs that were encoded with the auto generated cutlist. This is not the case for any new jobs that are trancoded with my cutlist, then encoded.