Back to the paint mismatch...theres nothing there that means anything.
As has been said VA leased a/c to skybus so i am sure they still have parts in old skybus colors. Maybe the cowl was damaged and the only replacement at that moment to keep that bird flying just happened to be off one of the skybus birds which had yet to be painted. It happens, i know we have done it...with smaller parts of course, Republic did it quite a bit when they flew for us...couple birds had cowls off some of their birds not painted in F9 colors because they were available and needed to be replaced asap to keep the birds going.
Nothin' wrong with it.