I'm getting messages from Apple that iCloud backup is full but it shows I have 3GB left

I just started getting emails from Apple that I won't be able to send or receive messages thru my account because I have exceeded my storage capacity. When I go to the iCloud settings and go to manage my storage I see I have 3.1GB remaining. I called Apple and they said I need to clear out my folders in mail. I told her it says I only have 376mb of mail in my backup. She told me I needed to clean out all of my folders, which I pain stakingly did but I get an email this morning telling me I have the same problem with storage but I still show over 3GB left in my storage. Has anyone run into this? What am I supposed to do? I feel they are making me upgrade before I need to.