When you say your "thyroid levels" were low, I'm assuming they were checking your TSH levels? If that's the case, too much TSH is HYPOthyroid, as in you don't have enough thyroid hormone in your body. When you don't have enough, you have problems losing weight, you feel tired, you have dry skin, and a whole host of other problems.

HYPERthyroid is too much thyroid hormone, indicated by low TSH levels.

And yes, you can essentially be "allergic" to carbs. Maybe your insulin resistant? Maybe you're devoping diabetes? Who knows, really, until the docs run more tests. But in any case, eating more carbs does cause a lot of people to feel more achy because it increases your inflammation response.

Just keep on lowcarbing and talk to the doc abour all your concerns.