Sorry for the delay. I wanted to take the time and do some testing with this issue to see if I could nail down the cause.
It does seem to be affected by the Mark Out point that we are applying. I will be passing this on to the Team in the hopes that we can get this resolved on one of the next updates.
In the meantime, do you have the ability to shorten the file outside of MediaShout before you bring it in? That way, we can leave the Out point as it is. That should help with this issue.
I hope this helps!