Time Machine is simple and doesn't backup to the same drive your are booting from.and it has been always like that. If you want other options then you need a 'cloning' software like Carbon Copy Cloner.
Open TM preferences->Options, now click on the plus button to add your HD.
This only works if you are trying to back up your start-up HD, as Satcomer said you cannot backup "to" your start-up HD.