Ok, now I can imagine what is going on.
If you copy an icon between VIs (independent of how you do it (drag and drop, CTRL-C & CTRL-V) the layers are not preserved. The entire icon is copied as one user layer (Text, Template and User layers are merged into one single user layer).
In 2010 the IE won't have any big new features (just some tweaks here and there), but an additional Copy & Preserve Layers menu tag might be interesting for one of the future versions though!
In the other case, where the icon looks different from what the IE is showing, I can't really explain what caused the problem, but as a matter of fact, the 'flat' icon is different from the saved icon editor structure. I am gonna take a look at this in the next couple of days. Probably I can be smarter on the IE side to avoid such a behavior.
