I saw the same here, so I set the packages linux-raspi2 linux-image-raspi2 and 
linux-headers-raspi2 to hold (as mentioned above) and reinstalled the last 
working kernel 4.4.0-1034:
 dpkg-reconfigure linux-image-4.4.0-1034-raspi2

My test with the latest version 4.4.0-1040 still shows the same bug.

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https://bugs.launchpad.net/bugs/1652270

Title:
  Could not boot into RPi3 with kernel 4.4.0-1038-raspi2

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