I have noticed that my encoding time decreases when I crop the borders of the stream in settings/Advanced/Clip Frame a mask the Borders.

Am I right?

It sound logical to me, because the encoder hasn't to interprate (encode) the borders of the source material.

I'm very happy about this because the encoding proccess takes several hours less then before.

__________________
just ask Jack

You're right Jack
You might want to start using GripCrop from SansGrip's filter collection.
It does all of that automatically for you.
Check here: http://www.kvcd.net/forum/viewtopic.php?t=2292

-kwag