I have had this problem with both Jordis and Aela. When they are first used as followers they can both carry a certain amount. After a while, they cant seem to carry anything extra. Any ideas? Yes I gave them upgraded armor, but even accounting for that, something is up. Its almost like when I take stuff from them, it is not being deducted from their carry weight total.

Check their inventories thoroughly too see if you didn't mistakenly place abunch of dragon bones absent mindedly or anything else heavy that you might have overlooked. Try taking out all their inventory if that does not work and see if they are still over encumbered. if so its a major glitch.

Have you ever dismissed them then rehired them? That spawns an extra invisible copy of their default armor in their inventory. It is another bug in Skyrim.

I have read somewhere in this group of forums, that when you really load them up, there ie a glitch that "keeps" a false entry of some of the weight. I don't know if that is true or not.... Dismissing someone really does seem to gimp their carrying capacity. I did that with Lydia on my last build, and she could barely take two weapons.... Really svcks, as they make excellent mules. But I will say, Aela is dear to me, her ai matches my archer very well for the most part.

They spawn an invisible bow/default armor when you leave 'em. Very annoying. There's a couple mods for it if you're on PC; if not, just avoid leaving them too much.
Not sure if wabbajack will solve this one (worth a shot?), but it does solve the level-up issue if you're also seeing the follower get weaker. Just (save, then) tell them to leave, use it, and it'll reset them to updated level when they return to normal.

I tried to remove all of her inventory but the 'taking all' command doesnt work with her, you can only take what you see. So she is ruined as a carrying helper?