the capacitor on the output is a normal thing yes, however it should rapidly discharge itself
as for the power supply, was it working previously?, for unknown reasons some models of power supplier will not wake up with shorting those 2 pins, (maybe uses the 3.3V sense line as a safety check) though rare in my own experiences,
as for the 12V rails, mainly its just a marketing term and they actually end up tied together on the same regulator 90% of the time, so no for series, so yeah, like the others have said, this wont do, there is a way to make an ATX supply float, but really, you wouldnt want to,