The only issue is that with these new seamlessly branched DVD's, if you're a purist, you're not actually getting the theatrical versions. There were some FX changes made for the extended editions that they didn't bother to change for the theatrical. For instance, in Fellowship there's a car in the background of one shot in the field. For the extended, they took it out, and now it's gone if you watch the theatrical version on the seamless branching DVD's.

And there's something similar on Two Towers, some landscape changes that were not replaced. I believe this is accurate....