Hmm, IMO, if you've been transitioning for 3 years and have used heat weekly, chances are, it's probably heat damage. It's hard to tell for sure - your hair could just be growing slowly. It might help to know how much of the ends are straight and to see a picture. But to me, it pretty much sounds like heat damage. I'm transitioning and this is my 15 month or so post relaxer and most of the relaxed hair is gone. I'm completely natural in the back. But have relaxed ends in the front and middle.
In terms of heat damage, I flat-ironed my hair a few weeks ago but was a bit reckless with one side of my head - I made several passes and ended up smelling my hair burning. Low and behold, I noticed that I have a bit of heat damage exactly where that happened. It isn't completely straight but the curl is much loser than the rest of my head.
HTH.