I don't know the cause and I haven't seen anything like this in the bug tracker. It seems to be related to arduino-builder so a workaround could be to use Arduino IDE 1.6.5, which was the last version before arduino-builder. You can get it here:
Another workaround would be to use the Arduino Web Editor:
You could also give the beta build a try, since there have been some significant changes to how arduino-builder works in that version:
but keep in mind that version is intended for beta testing and you may encounter some bugs.