Is this a vendor installation, for example a Lenovo machine? I know that IBM/Lenovo use a boot manager that is Linux based. The boot manager is used for things like recovery of the boot partition and also for running the maintenance utilities including the bios setup. It's not unusual to find vendor setups have two or three hidden partitions.
Might be worth running Diskpart from an elevated command window on your machine and viewing all the partitions, including the hidden ones.