The same applies the the theatrical versions too. Not so much ESB & RotJ but 'Star Wars' was altered in several small ways from it's initial release, to it's wider theatrical run and I think the re-release too. There may have also been some monkeying around in the TV and home movie versions too.Which version of the special editions would you go with? Pretty much every time they've been released they've had new tweaks made to them. I would just go with the most recent.
Same thing happened to the prequels, so without even bothering to count the SEs all of the OT movies have at least two different versions, if not more. There's just no pleasing everyone in this scenario.