I had some of the same issues I guess... I switched to a Rumba board, but could not get the UltimakerController to work with that no matter how I defined it en Marlin (best I could get was two lines of squares)...
So I bought a RepRap SmartController instead and got that to work easily... It is bigger though, so I kind of perfer my old Ultimaker Controller and its retro radio style box -_-
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Zapro 0
If you look at the schematics, you will find that the pin that the RepRap-panel uses for the kill-pin is defined as a 3.3V supply voltage on the UltiController.
The 3.3V supply is used to power the SD-card and level-shifter IC. To make stuff works, uncomment the killpin in your pins_RAMPS-file, and solder a wire from the 3.3V-pin on the Arduino to this pin. This will supply the UltiController with 3.3V for the SD-card and remove the kill-funktion.
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