Hi @obligator,
I just tried this out with my Yun and Chromebook, and it seems fine. What version of the library are you using? I tried the latest from Github (April release).
Using library Mozzi-1.0.3rc6 at version 1.0.3 in folder: /tmp/680337903/custom/Mozzi-1.0.3rc6
Sketch uses 8958 bytes (31%) of program storage space. Maximum is 28672 bytes.
Global variables use 1008 bytes (39%) of dynamic memory, leaving 1552 bytes for local variables. Maximum is 2560 bytes.
Validating license ...
Programming with: avrgirl-arduino flash -f mezzo_smooth.hex -a yun -p /dev/ttyACM0
resetting board...
reset complete.
connected
flashing, please wait...
flash complete.
wating for port ...
done
Could something in the sketch or library be crashing? Are you able to load other sketches like Blink to the Yun?