I was able to absorb the first dragon you kill in the game, but after killing my 2nd one which was a random encounter... i was not. I looted the body and now it is just sitting there and is not during to bones as i have not absorbed it is.. I have a 2nd shout which does not have a dragon soul so that is not the problem.

Must be a glitch,

Also...you may not be a Dragonborn. But a REALLY tough cookie.

Had the same Bug, but it did not occur again. All other Dragon Souls (16 so far) were absorbed without problems

Not necessarily your problem, but it seems that you need to supply the killing blow to get the soul. Once I learned that, I make sure the dragon kills all the NPCs in the area before I get serious with it.