Issue with ipod/mpeg4 encoding

I am trying to convert my dvd collection to mpeg4/ipod format. On some conversions, the encoding fps rate slowly drops to about 1-2 while the ETA goes up to 15 hours or so. I have tried using the dvd, hdd files, and iso file as source and the same thing happens. If I set it to 2 pass encoding the first pass does fine and then it bogs down on the second pass. I am using version

Hi Ivanh3
This should be running much faster. Check to see if the few movies that cause this problem have anything in common (DTS audio tracks selected, etc.) In 2-pass mode, the actual encoding takes place in the second pass, so that is why the first one does not show the problem. Encoding is very CPU intensive, so make sure to stop or disable any background stuff you don’t need and disconnect from the internet.

Thanks for your response. I don’t think it is a matter of an overtaxed cpu. The movies that do convert do so in about 1 hour. My machine is fairly current.
When this happens and the fps slowly goes down to 1, the program eventually stops encoding. The Eta will change from a really high time like 15 hours to zero. This takes about 5-6 minutes to get to this state.
No weird audio that I can tell. No DTS issues.
Again, thanks for yoru time,