I found a way to fix it. I was getting this problem with only "Showtime" T.V. Shows (Weeds, Nurse Jackie, Dexter). I found this odd because i download HBO shows that have a longer duration with no cutoff after converting the MKV file. It pisses me off becuase the converted file cuts off the last 5-7 minutes, which is the most suspensful part of the show. So I was up until 6 a.m. trying to find a solution, just so I could see the last few minutes of Dexter. This is the guaranteed fix.
1. Download mkvmergeGui (Copy and paste link). This will remux the file and create a duplicate mkv. It's easy, just select the mkv file. Once you have
selected the file, select "Extra Options" and select "None" for uncompression on both video and sound. Then click on start Remuxing.
2. Once the file has finished remuxing from mkvmerge, convert it through mkv2vob (no change required for options). Once it has completed, the new converted file will play in its entire duration.
I did this and realized I got 5 hours of sleep just to see the last unsuspensful 6 minutes of Dexter.