I have seen the same issue of no scheduled backups with both 10.11 and 10.11.1 on my MP (2013) with UPS attached and having the TM on an external TB connected drive.
Did a try with disconnecting the USB cable from the UPS, no change.
Then a reboot without the USB cable for the UPS connected, no change.
Did reconnect the USB cable.
Did a Restore Defaults on the UPS tab in the Energy Saver setting, immediately did the TM start and since have it been running on scheduled backups.
So don't know if it's just the Restore Defaults alone or a combination of the unplugging/reboot/Restore Defaults who did the trick.
But doing the Restore Defaults is a simple try out.