I some how forgot to paste the link to videora...
http://www.videora.com/en-us/Converter/iPod
Even though it might not help you since it is a PC program. (the program has a log so you can see what is going on but it might be too simple for your needs.)
As for your other questions. All the research I have done points to the fact that everyone does .mp4 files differently and their really is no rhyme or reason to how they do it. Like I said before I tested at least 5 different high end encoders and none of them came out with great results... some of the files worked in an iPod and some didn't. Since there are no guidelines it's pretty much a free for all.
You are experiancing what I have found... there are no rules. Just try different settings and find something that has a combination of the best file size, quality, and that the audio is in sync. Some work some don't, I wasn't able to come up with any similarites between what does and doesn't work. Some h.264 would work from some programs, some from another. Apple says to use QuickTimePro, but I even had issues with those files working on the iPod. The other factor was the starting file type; mpeg2, mpeg, avi, qt, wmv. They all gave different results.
So basically you just have to come up with your own method because nothing is right and nothing is wrong.
Did any of that make sense or help at all? Like I said videora worked really well after all was said and done, but it still had some issues.
