I found another female molex round the back of the case after searching online, the fan now spins. It still doesn't explain why the bios says there are no chassis fans spinning though.
Yes it does, you answered your own question. You have the fans plugged into to Molex connections. The BIOS can only read fan rpm when it gets that feedback from the 3rd wire when it's plugged into the MoBo Chassis fan headers. The bIOS can not read a signal that the MoBo doesn't get and since you powering the fans via the PSU molex connections, it doesn't get that signal.