MKV-Can't fast forward or skip chapter

I made a few Blu-ray movies into MKV files. I view them on the PC only. I use either VLC player or PowerDVD 8 for playback viewing. What I noticed is that when I try to skip a scene or move forward a little the movies freeze to the point where I have to close the players and restart the movie. I used Xvid4PSP for 2 of these movies and Ripbot264 for 3. Each one does the same thing when trying to skip through the movies. Is this normal or did I miss something during the encoding process? Other than that, they all play well if I just watch them through and sound is perfect as well as video. Thanks. Just curious.