I had exactly the same thing yesterday. Also solved it by updating and rebooting. It's a shame I cannot reproduce the issue anymore... Would be interesting to know what happened... Maybe the serial driver in the kernel was updated... I've had issues with serial ports between software updates and reboots before. Although in this case the serial appeared to be working (I even uploaded a new sketch, thinking of it now I never verified that the sketch was indeed running correctly... should have put some serial prints in there). Possibly the usb did not provide enough power triggering reboots on the arduino or something like that?