Yep I understand what you mean...As I've battled with 2 Avi's and Nero for the last couple of weeks....
You can try placing both files into Nero Vision and see if it comes out ok...Mine wouldn't the audio was out of sinc...
So I converted the files using Super and then placed them into Nero Vision and it finally worked...(make sure you use RW Discs or you may go through heaps of them)
This is the link for Super (it's free)
http://www.erightsoft.com/home.html 