Emulator

This applies to all games that use both the analog and digital triggers on the shoulder buttons to trigger different functions (off the top of my head, Luigi's Mansion does this and is affected by this too), but I'm just going to use Metroid Prime as an example.

In Metroid Prime, the L button allows you to do two things - lock onto enemies and scan targets (analog L press), and strafe (digital L press). I have digital L and analog L set to the same key on the keyboard (and likewise for R), and the game only does one of the two actions. It locks onto things when button-press threshold is at 0-99%, and strafes at 100%. (Separating the presses to two keys helps, but then the three-key limit most keyboards these days have comes into play.)

Now, I'm no programmer, but I'm guessing the game can't register both buttons being pressed at the exact same time - on a GameCube controller, it's physically impossible to press down the button fast enough for it not to register any analog input between 0-99 before reaching the digital press. By that logic, delaying the digital button-press by a frame (or whatever you can/have to delay it by) if the analog and digital buttons are set to the same key should fix it. (There may also be cases where you'll want to toggle a few analog pressures in between 0-100, but I'm not aware of any.)

Also, yes, this issue is tiny and nit-picky and probably not worth the time it'd take to fix, but it exists, and I've written a wall of text about it, so I'm gonna file it.

(3.0-637, OS X 10.7.4. Probably irrelevant, but whatever.)