Hi bbarberio,
In CWIS log on as admin and go to Scan>Folder and select Edit fo rthe user in question
Then choose from the dropdown what you want the passcode used for
If this is not the answer to your issue we need a very clear understanding of what it is you are looking to do as this is the only Passcode I can think of that applies to Scan To Folder.
You stated that " we have not used this Create a Folder option before to do this." So how exactly was the folder created that the other users are using when they don't use a passcode? You are going to have to explain this staement as the machine does not have folders by default, so "something" absolutely did this step.
In a typical workflow each user has a folder and that folder is created on the MFP through CWIS, if your location is different then we need a clear explanation on what you have in order to help fix that issue.
Screenshots and details about what is being selected at the MFP would help greatly.