El Capitan bootable external Hard Drive not recognised

Hi have two Macs - Macbook Air and Mac Mini.

On both Macs I had installed a clean Yosemite, and the created bootable backups on external HD (USB), following the advised from: http://osxdaily.com/2014/10/16/make-os-x-yosemite-boot-install-drive/ >>> creating a GUID partition etc. All was working fine in Yosemite on both machines.

Both external drives have loads of space let and are plugged in either directly into the Macs, or through a very powerful USB hub.

I have now upgraded to El Capitan (unfortunately both...) and the Macs will not recognised the HDs as bootable drives. Both HDs on both Macs.

The HDs as such are seen, meaning their icon is shown on the desktop and I can also see them in the Startup Disk window. I can browse the content, too.

However, when either setting them as startup disk from the preferences, or when holding down the Option key on startup, the disk is not shown, or listed. Thus I cannot boot from that HD anymore.

I have already zapped the Pram, but it did not help.

Any other suggestions?