A. If during setup up get the message:
Setup has performed maintenance on your hard disk(s) that requires a reboot to take effect. You must reboot and restart Setup to continue.
Press F3 to reboot.
This is returned when the Autochk part of the installation was able to repair the partition, but will require a reboot.
For a FAT partition, this could include corruption of extended attributes was fixed, the dirty bit was cleared, orphaned long filename entry was fixed (or any other fixing of lfns), directory entry fixed, crosslinked files fixed, non-unique filename uniqued, or any other structural issues at all fixed. There will of course be other specific "fixing steps" that would cause this for NTFS, or other non-file system specific structures.
In short this is not a problem as long as the setup does not get stuck in a loop keep running this stage.