That could be because freshly flue cured tobacco is high in sugars. Over time (especially after being bulked) the sugars convert into reducing sugars. Reducing sugars are basically a "regular" sugar with an aldehyde radical attached to it. Aldehydes are the flavor and good smell things that food chemists like so much.
Yes, something is definitely happening there. I have a tin of Samuel Gawith's Grousemoor (steamed and slightly stoved flue-cured), which originally was bright lemon-yellow. I liked the aroma then, but found it burned a bit harsh and hot, with blackish ashes, and a note of burned sugar. I forgot about it for a year. A few weeks ago I opened it again, and the colour had changed to a beautiful orange. It is really smooth now, ashes are white, no bite, slow burn, really good now in any respect.
I wonder what the mechanism of aging is in flue-cured. One year in a moist environment (the tin dried down from rather wet to ideal moisture) makes a world of a difference.
My own flue-cured Orientals went through a similar colour change, but mostly the leaves on the outside of the bunches. (Storage is rather dry, though).