Sounds like a system issue unrelated to your graphics card.
Have you updated the Motherboard bios to the latest version? Speak to the manufacturer for assistance updating.
What USB Devices have you got connected? Does the system boot quicker with them disconnected?
No - I build my systems myself.
I solved #1 by updating the BIOS of the graphics card - so the manufacturer of the motherboard was correct.
Regarding #2 I am in contact with Supermicro but it is not solved up to the moment (updated to the latest version right when I installed the MB).
And #3 is a "feature" of the board which can not be switched off.