Problem Encoding Blu-Ray Video

Hello,

 I'm having a weird problem with my encoding software.  I ripped the .mkv file from the disk with MakeMKV, and then it plays fine, but I decided to encode it to save space.  I followed the direction word for word on Lifehacker's website on this stuff (http://lifehacker.com/5559007/the-hassle-free-guide-to-ripping-your-blu-ray-collection), and this peculiar problem occurs.  When ever I start to encode the video, it freezes at around 1 to 2 Percent, and it changes to say "Que Finished".  It gives me the new file, and when I play it (in VLC), it works, the black bars are cropped, and it looks good, but the time at the right side of the screen (the one that tells you the total time of the video) reads "00:00".  I tried encoding on two different programs (Handbrake and VidCoder) and they did the same thing, so I think that it's a hardware problem (or some really weird software problem)

 Thanks for your help!

 

Edit: I forgot to mention that VidCoder tells you that it has failed, but Handbrake goes on like nothing happened. I searched everywhere online for this, and I seem to be the only one that has this problem.