Windows parititon not showing in Clover

[SyntheCypher]

My OSX Yosemite parititon recently died due to Invalid node structure (corruption) so I decided to reinstall to the same partition with El Capitan and update the bootloader to Clover.

I installed it all successfully and can boot to the new OSX partition from the Clover bootloader installed on the EFI parititon. However, now the Windows partition isn't showing in the Clover boot menu.

Any ideas on why just this partition isn't showing?

All the other partitions are showing including the external NTFS FILES parititon.

These are my partitions shown in diskutil.

synthecypher@prophet-osx  ~  diskutil list
/dev/disk0 (internal, physical):
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *500.1 GB   disk0
   1:                        EFI EFI                     209.7 MB   disk0s1
   2:                  Apple_HFS OSX                     249.5 GB   disk0s2
   3:                 Apple_Boot Recovery HD             650.0 MB   disk0s3
   4:       Microsoft Basic Data WINDOWS                 249.7 GB   disk0s4
/dev/disk1 (internal, physical):
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *4.0 TB     disk1
   1:         Microsoft Reserved                         134.2 MB   disk1s1
   2:       Microsoft Basic Data FILES                   4.0 TB     disk1s2

 

[SyntheCypher]

Just noticed in Clover Configurator that for some reason by default it is hiding a volume called Windows along with \EFI\BOOT\BOOTX64.EFI.

I removed the entry Windows entry and it showed up in Clover. (I'm not sure if this is the right partition maybe it's Window's EFI partition?)

In the Clover boot menu it said Boot to Windows from WINDOWS, when I tried to boot to that option it just when to a black screen with a blinking cursor (_) at the top left. So I'm guess this isn't the right partition?

 

[SyntheCypher]

In my EFI partition I only have the following folders, should I have a Microsoft directory as well with the Windows boot file?

 

[Going Bald]

Not if on separate drives.
Windows will have its own EFI partition on a separate drive if it is installed UEFI mode.