I've also just remembered, the second PSU started up on its own (psu fan started up) even without the dual PSU connector plugged in, all it required was plugging the molex connection from the PCI-e extender into the second PSU.
Any idea why this would be the case? It resulted in the same thing though just start up and then gives up after 5 seconds.
EDIT: one more thing I noticed was when I removed the 4 pin power connector from the motherboard and turned the PC on it starts up like expected (although doesn't post a signal to the TV screen I was using), and also the second PSU and GPU started up and didn't turn off.
This is my motherboard I am using
http://www.asrock.com/mb/AMD/FM2A88X-ITX+/
Thanks