Hi Daniel,
Oh no! There was a copy-paste error in the first expansion, it was supposed to be:
Series[Exp[-Pi Hypergeometric2F1[1/2, 1/2, 1, 1 - x]/Hypergeometric2F1[1/2, 1/2, 1, x]], {x, 0, 5}]
and you can test the following by series expansion:
Exp[-Pi Hypergeometric2F1[1/2, 1/2, 1, 1 - x]/Hypergeometric2F1[1/2, 1/2, 1, x]] == EllipticNomeQ[x]
So that first one actually seems to work okay. The other three expansions are more of a concern, they come from Ramanujan's theory, and appear as examples in Bruce Berndt's "Ramanujan's Notebooks Vol. II" ( on p.80-82). Does your fix cover those examples as well?
I may be around the office tomorrow afternoon if you want a better explanation, or to see a few more examples I've cooked up.
--Brad