With the external attached run the command below and tell us what it says. This will show the volume layout.
It may be that the El Capitan install turned the drive into a core storage volume that we will need to revert.
Sorry to hijack this thread, but I have a similar problem and I think the El Capitan partition I made got turned into core storage... I got this readout when I ran that command through terminal.
/dev/disk0
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *500.3 GB disk0
1: EFI EFI 209.7 MB disk0s1
2: Apple_HFS Macintosh HD 413.6 GB disk0s2
3: Apple_Boot Recovery HD 650.0 MB disk0s3
4: Apple_CoreStorage 65.2 GB disk0s4
5: Apple_Boot Recovery HD 650.0 MB disk0s5
/dev/disk1
#: TYPE NAME SIZE IDENTIFIER
0: Apple_HFS El Cap *64.8 GB disk1
Logical Volume on disk0s4
B6F22C30-3023-4EF6-8BF7-0D627916868E
Unencrypted
UPDATE: Disregard... Reverted the partition from Core storage back to regular storage and we're ok.