Hi Paul,
This extra partition you are reffering to is this the recovery partition at the end of your OS disk? (890MB in my example)
This one is not acctually empty, it contains the Windows Recovery enviroment (WinRE)
running regagentc /info in an elevated terminal will show this
You can remove this partition (disabling WinRE for recovery purposes)
Any OS upgrade or repair will resotre it
hope this helps,