When your run the fixmbr command from the Recovery Console, you receive:

This computer appears to have a non-standard or invalid master boot record. FIXMBR may damage your partition tables if you proceed. This could cause all the partitions on the current hard disk to become inaccessible. If you are not having problems accessing your drive, do not continue. Are you sure you want to write a new MBR?

You can ignore this error.

After you run the command, and it works, you will receive:

Writing new master boot record on physical drive
\Device\Harddisk0\Partition0.
The new master boot record has been successfully written.

NOTE: Even though you receive the subject error every time you run fixmbr, ignore it, as fixmbr can safely rewrite the MBR.