I could run it in a 12x12 config, but opted for 2x22 which gave me 44 inputs.
Right, but you can't do that with a KE-18, only 18x1 or 9x9 inputs (no 16x2 matrix, for example). And it's not programmable. (Actually, it may be 17x1 as one of the "outputs" may be GND.) And 9x9 will have ghosting problems. See
http://www.mameworld.net/emuadvice/keyhack2.html under "Common Misconceptions" for an explanation of ghosting.
Basically, what it means is you can't press certain combinations of keys at the same time. So, with a KE-18, you end up with 17 independent inputs in non-matrix mode, enough for a SF layout, but without coin or start or esc keys. Matrix mode is basically unusable, b/c you would only have 9 non-ghosting inputs and if you only needed 9 inputs (a simple joystick and 5-button layout) you wouldn't have more than 11 other keys (start, coin, etc) so independent mode would work here as well.
Also, the KE-18 is non-programmable. This doesn't matter for MAME as long as all the default outputs are assignable in MAME, but could be a problem if you wanted to use other (primarily DOS) emulators with the KE-18.