I'm not sure what you are getting when you try to perform a chkdsk /f
In 1607 in the registry -
HKLM\SYSTEM\CurrentControlSet\Control then click on SessionManager you will see an entry for BootExecute in the right pane.
To the right of that is autocheck autochk *
But in 1703 the entry is -
autocheck autochk /p \??\c: autocheck autochk *
and even when you remove the first part of the string the chkdsk /f still won't execute after the reboot.
I've done a repair install on this machine and on checking that key, I found the registry expanded from HKLM which suggested something wasn't right.
That key was just showing as autocheck autochk * but when you try the chkdsk /f it still fails and when you go back into the registry, the first part off the string has been reinstated.
I'm not too bothered about that for now as I can still do it in the Recovery cmd prompt, but I've found I have a bigger problem.
Last night I found that I couldn't get an Internet connection in Safe Mode with Networking - it keeps taking out my Ethernet and in Device Manager/Network adapters, the Properties of the Ethernet reports Code 45 - This device is not connected to the computer.
To reinstate that, you need to run the elevated cmd netcfg -d and a reboot, but it also takes out the Ethernet on a repair install and did it when I first upgraded to 1703.
In 1607 you can manually connect wireless in Safe Mode with Networking through the wireless icon in the system tray, but in 1703 on mine that icon is dead and doesn't show the SSID(s) so that you can connect.
I don't know if you also have this problem but I'd advise you to roll back to 1607 to see if your apps problem has been fixed and wait for it to come through WUs, but you'll know when you are going to get it through the phased roll out, you first get an update for your privacy settings.