I did not come up with this fix- a fellow Steam user did. Here are his/her exact directions that I followed to solve the problem:
I'm not sure WHAT in the steps did the trick, but here's how I got it:
1. Install (re-install?) Vjoy, a joystick emulator.
2. Set up the buttons (Right, Left, Up, Down, Z, X, C, V, W is what I used, as per default)
3. Enable Vjoy, and turn on key blocking.
4. Open Recettear's key configuration tool, and set the gamepad controls (even if they're the same)
5. Open Recettear.
6 (optional). Turn off Vjoy.
Now it even works when I turn Vjoy off.
I'm pretty sure it had something to do with one of the registry changes Vjoy makes when you install it, then..?
Andrew Dice might want to contact Ben Baker for a look at the code.
Get back on me on whether this works for you as well; I think I might've just solved a problem that nobody's been able to address since 2010.
Yup, I got it to work.
That being said, when I completed this fix, I lost all local Recettear data. HOWEVER, I do not know if this is a result of the fix, or something else. However, if you were in my position with Recettear not working for 4 months, that shouldn't be your largest concern.