The link for the manual wont download on my computer but I have found the specs for the board and as you say there is a 8 pin atx & a 6 pin atx there is also a 4 pin atx specified----"ATX-power supply connector
8-Pin ATX2, 6-Pin ATX1, 4-Pin ATX3" as you can see from the spec http://eu.shuttle.com/archive/en/fb81.htm so according to this you should have a spare 4 pin atx connector coming out from your psu this is not a molex plug.
Update found the M/board info and it does seem that you have not got the 4 pin atx connected, there is a fan connector very close to the 4 pin atx and you could possibly confusing this as the atx.