This happens cause mods (or Forge) are  setting different Id's for the exactly same blocks in different worlds. And when i'm trying to copy an item with blocks added by a mod into another world, those blocks transform in a very ramdomly way (e.g. iron half-slab became a water source block in a new world). At the same time copied blocks loose all their TAGs when they are being loaded in minecraft. This affects any mod, which creates TAGs for it's blocks, such as Carpenter's blocks, Project red and others. Does anybody know how do i keep the same ID's on different Worlds in order to move modded objects between those? 

Tell MCEdit to update. We've stored the ID map for the last 4 years or so. It wouldn't be hard for them to read it and put the correct ids in.