I assume we post bugs here... if not, someone please point me to the right place!
Regardless of the state of the "Verify Code After Upload" checkbox in Preferences, the code sent to the Due is always verified. A little bit of troubleshooting on my part revealed that the culprit is the '-v' flag that is always passed to 'bossac':
bossac.exe --port=COM30 -U false -e -w -v -b [temp_filename] -R
If this command is run manually without the -v flag, verification does not occur.
This bug occurs on Windows in both the beta and the nightly build, I can't vouch for Linux or MacOS. The verification takes several seconds to run even on a small sketch so it's nice to be able to turn it off.