I actually was under the impression that certain medical conditions, particularly mental or neurological conditions that affect the chemical structure of the brain, can actually cause akathisia.

It sounds like it could be your medication, there are other things that can cause akathisia as far as I know. A lack of iron, or insomnia seems to play a role in some people. Things like that could help 'push' you into it, if you get what I mean. People with mental disorders like depression or manic depression often seem to have problems sleeping, so it could be you're getting the akathisia from a different source. I would ask your doctor about that, and ask if in their opinion it was solely due to your medication, or if other factors could have contributed.

Oh, also, I had really bad restless leg syndrome while I was on a Effexor for whatever reason. I also got it pretty bad when I had a withdrawal from klonopin, but I think that is pretty common. None of my bouts with it lasted for too long, but it was enough to make note of.