This is coming from the log file on first boot:
[Input] Warning : N64 Controller
#1: SDL joystick name '(null)' doesn't match stored configuration name 'AutoKeyboard'
[Input] Warning : N64 Controller #1: Disabled, SDL joystick 0 is not available
[Input] Warning : N64 Controller #2: Disabled, SDL joystick 1 is not available
[Input] Warning : N64 Controller #3: Disabled, SDL joystick 2 is not available
[Input] Warning : N64 Controller #4: Disabled, SDL joystick 3 is not available
After messing around with the most recent available copy, I've found I cannot configure my controller. I am unable to assign POV Hat directions to anything -- The word "null" is replaced with whatever I named my configuration when I try to tamper with it.
The controller is a third-party model made by Power A, marketed as Pro Ex Wired (USB), billed for use with PS3. As with any third-party product, it is fraught with issues using software made for brand-name product, with this being no exception.
Error is resolved by tampering with InputAutoCfg.ini, using instruction from the m64+ Google Code project page and SDLJoyTest, but it is quite inconvenient for new users, and quite a dumb issue for something that is suppose to remove the hassle of using the command line.