What software and version do you use to rip? I suggest you rip in full mode unless you know which title you want to rip. DvdReMake does check if the ripped files have any problems or not.

Well, actually, you can do what you want with DvdShrink. American Gangster's is a case of multi-story title. That's why you see 2 titles fall under Main Movie. The shortest time title (Title 2) is the theatrical version, and the longest time title (Title 1) is the unrated extended version. So just include the version you want and the deleted scenes from disc 2 in Reauthor mode and you should be OK.