Fortinet file system check recommended

When ever I log in to my fortigate 51E I get the following pop up (cant attach image for some reason): 

                                                  File System Check Recommended

The last reboot was triggered by a power disruption. The system is up and running, but the undefined disk may have issues.

It is strongly recommended that you check the file system consitency before proceeding.

                                           Reboot and scan disk now | Remind me later.

I pressed the reboot and scan disk now option on two occasions, when I select it, the system goes offline and scanns (I assume) but when it's done and I log in again it still gives me the same pop up message. Any ideas on how to get rid of it?