When the NOOBs method of creating an SD card for Raspberry Pi came out, we began to get reports that the AlaMode setup caused the Pi to crash (kernal panic, etc.)

At the time, I didn’t have time to look at it and just recommended sticking to the pure Raspbian image.

AlaMode setup now works for NOOBS as well as Raspbian. Updated links, and instructions are on the getting started page  You can grab the updated setup bundle at:
http://git.io/alamode-setup

Note that this script references install locations for the Arduino IDE that have only been verified for the Raspbian distro. NOOBS allows you to install other distros, but this will probably only work for the raspbian option (tested) and the other raspbian variants (such as scratch).

The problem was in turning off the console output to the serial port (used for programming AlaMode) we overwrote the cmdline.txt which controls booting. Because NOOBS isn’t a pure linux image, the partitioning of the SD card is different, and the referenced device for where the linux Kernel lives was incorrect (it was correct for pure Raspbian).

If you’re curious, this was fixed by using sed (stream editor) to remove the console references, leaving partitioning references intact.