Had this happen twice, in my case the pi booted from SD but pointed at external disk /dev/sda1 My solution was to boot from a different SD card only and make sure the HDD was not mounted... Then fsck /dev/sda1 e2fsck /dev/sda1 In both cases when it happened and I did this procedure it stopped the pr...

Had a similar issue.. a new raspian and fresh complete install and like magic it was working.. Interestingly enough I had the same symptoms.. just flickering, and perhaps the same cause: I had installed a USB based audio device..

Great that its working now!!