I've been reading Trigun both via online scans, and now in the books I purchased (dark horse) for the different translations, and noticed in volume 13 - 14, there seem to be some differences, There is no overall changes to the plot, just some fight scenes are extended/reduced, the same with some dialogue, while some panels have been re arranged a bit.

I've checked google and couldn't find any reasons why this may be. The online scans appear to be consistant with others, unlike the books.

Im not sure why that is, but the book might be a special edition, like a kanzenban or something

I think that this is common when the manga goes from magazine to the trade paperback editions. The manga creator is usually working under insane deadlines (for Trigun, Nightow was drawing 40 pages EVERY MONTH). When the volume of the manga comes out, it's a chance for the creator to take a step back and look to see if there is anything that needs to be tweaked to make the story flow more smoothly. Sometimes drawings are added, sometimes they are taken away.

Check out my website on the manga: http://www.trigunabridged.com