When Windows Recovery Environment (Windows RE) is booted from a source that is not linked with the currently installed OS, Windows RE is unable to verify the Boot Configuration Data (BCD) boot entry for the current Windows installation. As a result, a new BCD entry is created for the Refresh process. On the first reboot of the Refresh process, two boot entries will be present in the BCD store for the same instance of Windows 8. As the Refresh completes and Windows boots into the refreshed environment, Windows is able to determine which BCD entry is needed and the duplicate entry is removed.
Example Scenarios:
Boot from the Windows 8 installation media:
Confirm Regional settings
Select "Reapir your computer"
Select "Troubleshoot"
Select "Refresh your PC"
Click Next
Select "Windows 8"
Click Refresh
At this point the Refresh process begins. On the next reboot two tiles for the Windows 8 installation will appear as boot options. Selecting either will allow the refresh process to continue. On the next reboot the default configuration of no boot menu appearing will be restored.
Boot from Reapir USB Flash Drive or on Disk Windows Recovery Enviroment.
Select keyboard layout
Select "Troubleshoot"
Select "Refresh your PC"
Click Next
Select "Windows 8"
Click Refresh
At this point the refresh process begins. On the next reboot two tiles for the Windows 8 installation will appear as boot options. Selecting either will allow the refresh process to continue. On the next reboot the default configuration of no boot menu appearing will be restored.
NOTE: This issue does not occur if the Windows Recovery Environment associated with the Windows 8 installation is used. Examples of ways to accessing this environment is choosing to boot to Windows RE from within Windows, or if Windows is unable to boot it will automatically boot to the Windows RE environment associated with the currently installed OS.