I don’t see any errors as such in your conversion you’re running into the GOP framing issue.
Also please update to the latest BETA version as it has a few updates which may help you.
There are a few things we can try to get around the GOP issues, so lets start with the first:
I see that your profile doesn’t have:
PreConversionCommercialRemover=true
The CommercialMergeTool=avidemux option only works if the above option is enabled for non-TS profiles.
Try adding the above options and then re-run your conversion and if you’re having issues post your conversion log back here.