Mark Wilson's emulator defaults to allowing you to toggle the lights, but in case you want it to work just like the original Kenbak-1, he included a way to make that happen. If you execute a SYSX instruction (0360) with 0210 in the A register and 0 in the B register, it will change the behavior such that you must use CLEAR. If you repeat that instruction but with 1 in the B register, the toggling behavior is restored. Here is the relevant paragraph from Mark's emulator documentation:
010: Flags controlling the Kenbak-uino.
Currently only 1, if b0 is set, pressing one of the Data switches *toggles*
the bit, otherwise it only sets it (as per the
KENBAK-1).
Here's the code (starting from 0):
210
000 [change to 1 to enable toggle]
000
004
360
000
343
004