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In both Fusion and Zero I can not do the following:

- diagonally aim down while running to the left and shoot (samus will aim at the ground only)
- hold a charge, run to the left, and jump (only run with a charge; falls straight off ledges, etc.)
- screw attack to the left with a charge
- run to the left while firing missiles

I can do all the above to the right, however. What's the dealie? Seems to happen in all versions.
Thread title: 
That'll be your keyboard. Try moving your control setup elsewhere on the 'board.
I'm guessing it's some random nuance of VBA because I use the same keys to move in other games (like CS).
I find that if I have all the buttons on one side of the keyboard, it will only register the first two or three.  If you know anything about electronic pianos... they have a thing called polyphony.  What that means is how many sounds it can play before not registering any more.  I think some keyboards work along the same lines:  only registering so many simultanious keystrokes at one time in one 'zone'.  Try spreading out the keys that you use (have the a,b,l,r on the left and have start, select, and the directions on the right) That might do it, or just invest in a decent controller.

[/useless info]
I have the exact same problem as Snow, except doing everything to the right doesn't work for me. After I changed my shooting button to one key to the right, everything worked fine, but it might take a long time to get used to.  :(
How do you people play on keyboards?  I just know nothing good could come from me trying to play Metroid anything with a keyboard.  o_o
I don't know exactly what causes this problem but i've expierenced this in other programs aswell. There are 2 possible causes:
-the keyboard doesn't send info of more then 3-4 buttons to the PC it just ignores if more a pressed
-The keyboard event handlers of the used programming language limit it to 3-4 buttons.

Its probably the latter option. And it sucks!
/me loves his control pad
I have the same problem right now.
Reinstalled vba so now i switched controls. I didnt use to have this problem (and these new controls is way less comfortable so im switching back). So my guess is that you have to switch controlers!
Through sheer luck, I managed to get a key combo that works very well for me. But it might not work on your keyboard; I've noticed my old keyboard allows me to press combo's I can't use on my new one, and vice versa.

Anyway, I use this setup:

D-pad: Numpad 4-5-6-8
Jump: S
Shoot: A
L-button (aim): Numpad 7
R-button: Numpad 9

No conflicts at all on my keyboard.

I also heard turning sticky keys off helps, but it doesn't appear to do wonders on with my keyboard :P
This worked for my keybord

WASD- move
4- jump, 5- shoot (or the other way around  :?)
8- select
6- er.. missiles
7- aim diagonally
start- i prefer enter..! (the small enter) but it really dont matter.. I dont use it very often.
The trick is to use keys that the computer recognizes as combination keys.  Control, shift and enter tend to work very well in multiple key-press situations.  I usually use the numpad for my movement.

Of course, I don't play any GBA roms, so there may be more keys to register than my layout could help.  Or fewer, I guess, if we're using the SNES as a gauge.