I see the purple line you're talking about. It's extremely subtle. I can't find any reason for it, though the encoding process for V2 of LOE was less than ideal. It should not be a problem now that my workflow has been fixed, but I'll keep a sharp eye on that in the results.

About V3 changes, most of them are described here: http://originaltrilogy.com/forum/topic.cfm/Star-Wars-Episode-III-Labyrinth-Of-Evil-Finished/post/727517/#TopicPost727517

There's a few more things, like removing another instance where Obi-Wan addresses R2 by name, and other tiny tweaks.