Sounds like you may have encountered a known limit on the number of folders that you can have. See if this report matches what you are experiencing:
For More Information see: 51 Layout Pop-Up Menu Folder limit…
This is one of many acknowledged bugs that can be found in the Known Bug List thread here in the Report an Issue section of the forum.
It can also be downloaded as a database file from: https://www.dropbox.com/s/jt09b82i0xijbu3/FMP%20Bugs.zip