I had the same problem initially. It would seem the original ISO image is somehow more compact that a newly built ISO image. You want therefore to mess as little as possible with the original ISO image, so do not "unpack" (to hard disk) and "re-build" (from individual files and folders) the ISO image, but add and substitute (as few files as possible) to the original ISO image, all within the MagicISO or UltraISO environment (I use MagicISO, by the way).