MTV Recording Showing Wrong Show Length

For the past two days I have recorded programs off of MTV (TVE) and the wrong length is being reported but the entire program recorded. For example, I recorded Catfish for 60 mins, the show recorded in full. But the DVR is saying on 47 mins recorded. Same thing happened for another show. I recorded 1 hour but it shows the length of the program at 46 mins recorded. Decided to record the same program but recorded it for 90 mins, the dvr reported back it recorded 67 mins of the show but the entire show was recorded. I am not sure what is happening or why. Any ideas?

Yes, timestamps from TVE recordings are screwed up.

Had it happen even with a Cable recording from an HDHR Prime when the PMT and Vid/Aud PID's changed midstream during a recording, causing the recording to appear short because the PID's for the Video and Audio changed.

Does the whole recording play the full length?
In both a Channels Client and in the VLC Player?
Did you try fixing the timestamps in Channels or remuxing the recording with ffmpeg?