As I had supposed, the problem was the 'freights' material getting screwed up every time I updated crates' vertices. Don't ask me how.
I have tried every combination of import options not avail, and modifing material's extended data properties didn't work either: apparently after importing a new mesh extended data wasn't applied anymore.
At the end I decided setting a new material for replacing the corrupted one. It seems to work; at least Goblin renders the crates correctly. Please, check that in game everything is in order as well. New version of the fix below:
http://www.mediafire.com/?d8r83hwqtccrv9q