I'm so sorry that you're in such a state of confusion as your docs seem to be as well. It's always harder when even the docs are confused, isn't it?
Thyroid problems can be the most confusing aspect of this as it can really wreak havoc on our systems. Hypothyroidism can really knock our hormones out whack and what's equally baffling, I'm sure for the docs is that you're on birth control meds which also makes changes to periods, hormone levels etc.. The fact that you're getting periods still but, on birth control really makes one wonder if there is ovarian failure but, you're still getting periods because of the pill. That makes it "a which came first...the chicken or the egg" type of situation.
The thing is, our hormones are swaying all over the place at all times so, one test may not give a full picture of what is going on fully. At 26 years old, it's more likely that your hypothyroidism and birth control pills are throwing off these hormonal balances greatly and I'd be willing to be that if you were to have more testings done in the future, once they've gotten your thryoid levels in check, you'd find that those levels have changed yet again.
I'm not a doctor by any means and am only thinking logically and from what I've read but, if this were me, I'd continue on with BOTH your gynecologist and your endocrinologist and ask them to work hand in hand on this together for you. Try asking your gynecologist to talk this over with your endocrinologist and see if they can work together in coming up with answers to this for you. It does sound to me though that your hypothyroidism may not be fully in check and even if blood tests are coming back within normal ranges for thyroid function, they may need to fine tune this a bit more, based on symptoms rather than test levels.
Please let us know how you make out! Coming back and posting an update will help others as well. And, never forget that if you feel that you're not getting answers that are helping you or you feel that nothing constructive/helpful is being done, it's your right to seek out second and third opinions until you get someone to listen fully and be willing to work WITH you on this! :)