Come to think of it, the very first video I encoded I did on my work laptop with AV converter 4. It was horrid and the sound was off from the beginning. That said, I really, really think it is the software, not the player. Mainly because the only bad thing I noticed after watching two separate hour long episodes on my tiny little screen was a searing headache ;-) The videos were fine.
Try a couple other converters to see if they work. You can get a free trial of the one I'm using for Windows
here.
You may also want to look at one based on the FFmpeg code. I use that all the time on my computer to do all kinds of things like transcoding, joining, splitting streams, muxing streams, and so on. Granted, FFmpegX is for OS X, but the underlying code is the same, and there are many projects for Windows you can easily find using Google.
At least try one with the same one I know works. That will let you know if it's your software or player.