My users can't find their messages in the folders they put them in. We can search them in their Retain mailbox but they are not in the folder, they are in the Inbox.
Retain archives messages where Retain finds them. Usually what happens is that the message comes in late in the day and Retain saves them to the Inbox folder, which is where Retain found the message. Some users have a difficult time with that.
A way around this is to set the profile to wait a week for users to place items in the folder they want it in. However that leaves you without those items in the archive which allows for potential data loss.
A better way to deal with this is to run regular archive jobs during the week but have Retain run a different job over the weekend that goes back a week or two. That will cause Retain to update the location of items in the data. This type of job should go quickly as items do not need to be stored on disk again. For maximum performance the worker should be on the mail server so item do not need to be sent across the network.