Frequent CloneDVD2 error

I’ve been using CloneDVD2 for awhile now with decent success. However, I find that about 50% of movies I attempt to burn have errors and CloneDVD2 won’t go through the process with them, not even the preview screen. I usually try getting another version of the movie and hope it works but lately I’m finding the problem is worsening. Basically, I can watch the movie via Media Player with all menus and everything intact, but when I attempt to open it under clonedvd it gives me an error that there is an “unexpected end of file” or “IFO proerties error” saying that it was not proerly mastered or doesn’t contain all of the necessary files for burning onto dvd. How is this possible when I can watch it on Media Player? Is there a program out there that can re-master the files so that they are all correct and will allow me to burn it? Thanks in advance.