Nop, no bug here so far. I viewed my custom icons.bni from war2.me, rearranged a few, saved, reopened, it's fine. Also did "save as" to a new file, and that's okay too.
Also, what's the difference between flag & tag? Flag is linked to permissions? Can that be controlled in the config files? e.g. set which flag to use for admins? Or if I wanted to customize that, would I have to overwrite the 0x00000001 flag with a new image?