Sorry I had the answer here and haven't been around in a while myself.
Not sure what actually happened with your situation, but the resolution is probably this:
In d7II, click the Users menu, then the Internal User Account Mgmt option (see pic)
You *should* see even these invisible users that you aren't seeing in Windows user management mechanisms. They also probably have the "Hide User from Login Screen" option checked (see pic) which is why I suspect that was your issue - uncheck the ones you want to see on the login screen and manage in Windows.
This feature within d7II manipulates the registry key (below) which can be used to hide user accounts from the login screen (or used to be the official method used for Windows internal purposes pre-Win 8 I believe, though it still works.)
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Basically adding a DWORD there with the username will hide that user from the Windows login screen (and other management mechanisms like Control Panel > Users or the classic userpasswords2.cpl) while still allowing services and code dependent on those user accounts to function.
I'm thinking this area of d7II should be the only area within d7II which manipulates this registry key, so without using it specifically I'm not sure how/why this happened to you if it was some result of d7II or a 3rd party custom app you might have been using in conjunction with d7II, but stranger things have happened -- just please let us know if this has occurred again for you or does in the future and we can look more closely at the details of the situation.
Again I realize I'm late to this particular party, but just throwing the info out there for anyone else who may run into the issue.