Hey, just signed up to tell you that I found the culprit. Gish from the Humble Bundle had the same problem.
On my system at least, it was caused by a piece of software called Osculator, which is handy for playing with wiimotes, iphones, controllers etc. Specifically, it was the "perfect pairing" extension of that application that created some virtual joysticks which behaved weirdly.
The solution is to run Osculator, go to preferences, input tab, then uncheck "perfect pairing". This low-level extension may be there still even though you've gotten rid of the Osculator application itself. In that case, the solution is to download it again, run it and disable that preference. After that, you may uninstall the application, or keep it.
If you use Osculator, you can always disable perfect pairing to play Aquaria, then enable it later.
The author of Osculator was kind enough to help with this, and I've notified him of this post.