On some of those DVD's that you mentioned....I think those were DVD's which had an option to reinsert the deleted scenes in their appropriate spots. I think the original Xmen DVD did that...not sure if Xmen 1.5 does.
The only extended DVD's that seem to not exhibit such a problem are those which are genuinely restored to their Director's Cuts.
Terminator 2 The Ultimate Edition DVD had a hidden "third" version of the film which showed the absolute, uncut version of the film, even with the scenes that James Cameron felt were unnecesary for the Director's Cut. I don't think I noticed any transitional errors in this third version, and I played this on my Playstation 2. (The only bitch I have about the original PS2 models is that their drivers tend to wear out fast....and now, my PS2 won't read multi-layer DVD's anymore. I think the upgraded PS2's out now, and will rectify this problem.)
BTW, for those who may not be aware of the third "uncut" version of T2. Do the following:
(note: It must be T2: The Ultimate Edition DVD)
Start playing the "Director's Cut" of the film. When the film starts playing, go directly to the film's menu. (Do not hit Stop! Just hit the menu button.) Then, enter "03" for the title...and start the movie again. If this is done right, you will now be able to watch the "Extended Director's Cut" with another five minutes of footage in addition to the 15 restored to the "director's cut" and the "alternate ending" of Terminator 2.
I am pretty sure that was the procedure.
Respectfully,
General Chang
"So the Enterprise is on her maiden voyage, eh? Now that is one well endowed lady. Ah'd like to get mah hands on her ample nacelles, if ye'll pardon the bit o' engineerin' parlance." -Scotty, STAR TREK, 2009