Also seems to be directly related to how we use the fast switching to enter the admin credentials. Like the user who is logged in can enter their password, but when we try to switch to enter the admin name and password, that's when it's doing that weird deleting of anything I type.

Is the machine AD bound?
AD bound machines always delete whatever has been entered in the password field when they manage to get a live network connection (terrible piece of UI design by Apple), perhaps when you are switching user, for whatever reason the machine keeps losing and reaquiring it's connection to the AD servers, thereby repeatedly deleting the password field.
We have lots of 10.12.3 JSS and AD bound machines and other than the behaviour described above we have't had the issue, we also have fast user switching enabled which I use reasonably often.

Nope. These machines are not bound to AD.

Some (including myself) have had luck solving weird login window issues by making sure all of your "Login Window" and "Security & Privacy" settings are located in a single configuration profile. I seem to remember also reading about gremlins related to having the password requirement being set to "immediately" and that you may have better luck setting it to "5 seconds."

Either of these things apply to you? (Multiple configuration policies for these settings or having require password set to immediately)