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In some textures background is not background. It aplies to the object as wholesome, but some areas must be transparent and for that it is nesesary to fix alfa chanel mannualy. Some programs sees alfa chanels as transparent with opacity of 0% some sees them as transparent with opacity set to 100%, like iL2 do. You can all of that set in photoshop (and other aplications). For that purpose that links that vpmedia gave is very good.