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I haven't any big issues with Handbrake at all, I love it! I just use the preset's and let it be, no need to 2pass for me, everything looks great.
 
Google: Cucusoft

Here's what I use. I gave up on Hand brake a while ago. I did pay for this program and it works great. No BS, just stick your DVD in and hit the convert button.

I use iPod Setting 3 preset. It works great for iPhones and video iPods. No problems. Very happy with this program.

Here's the link: http://www.cucusoft.com/dvd-to-ipod.asp
 
I've used handbrake for 100's of conversions without problem. Maybe it's the PC version as mentioned earlier. My only issues were getting the settings right but with new versions, it's pretty much menu driven and dummy-proof.
 
Here's what I use. I gave up on Hand brake a while ago. I did pay for this program and it works great. No BS, just stick your DVD in and hit the convert button.

I use iPod Setting 3 preset. It works great for iPhones and video iPods. No problems. Very happy with this program.

Here's the link: http://www.cucusoft.com/dvd-to-ipod.asp

Only problem, is, it's Windows only, and it's DVD-to-iPod, which won't suit everyone (or even a lot of people).
 
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