The penultimate verse of Isis on the LP version (as MetroLyrics confirms) are clearly audible as follows:
She said "Where ya been?", I said "No place special"
She said "You look different", I said "Well, I guess"
She said "You been gone", I said "That's only natural"
She said "You gonna stay?", I said "If you want me to, yes"
I Binged this a couple of days ago because I wanted to pin down some lyrics that are mumbled (it turns out that "the borderline" is actually "the dividing line", not that it makes any difference) and was surprised to see that Bob Dylan's official site gives the penultimate verse as:
She said “Where ya been?”, I said “No place special”
She said “You look different”, I said “Well, not quite”
She said “You been gone”, I said “That’s only natural”
She said “You gonna stay?”, I said “Yeah, I jes' might”
This might be some bizarre copyright wrangle, where Bob Dylan doesn't have to hand over a share of the royalties if he publishes his own version of a song which he co-wrote, but FFS.