MKV conversions using Handbrake

[havash]

Hi there, I've been converting a whole lot of files recently to MKV using this guide:

http://lifehacker.com/5559007/the-hassle+free-guide-to-ripping-your-blu+ray-collection

I started off with Blu-Ray files, but now use this to convert normal VOBs I have. Everything seemd to be going fine, until I noticed that one file became stretched out. I found out it only does this stretching with Anamorphic VOBs which have a high GOP value. Does anyone know why this is?

Also, films which are widescreen, but non-anamorphic, get the black bars cropped off when I convert them. This is a good thing, but just wondering how it knows to do this.

Finally, why does the resolution number always change when converting using this method? It'll go from something like 720x480 to 718x400, why does this happen?

[Bonie81]

I have tried HandBrake 094, but having a same problems as yours.
If you try it again, HandBrake gonna give you something different than 718x400, which I could not figure out why?
Finally I started using MediaCoder.