I just tried to apply a bool modifier to a cylinder using three joined cubes as bool object ( see attached file). As soon as I select the object for the modifier to use, eg. the joined cubes, blender crashes.
The build I'm running is: c359343f8dae6689c955dc1fa700cb26f6cd2e95
System Information
Mac OSX 10.11.3
NVIDIA GeForce GT 750M