I recently rebuilt my rig on an ASUS P8Z77 WS Mobo and attached a Samsung 840 250 GB SSD for the boot drive and a Samsung 830 256 GB SSD for a secondary drive.
When I initally connected the drives, I contected them through the Marvell ports. I get really fast boot time (I'm in Win 8 64 Pro in about 4 seconds) but I've been reading that the Intel controller is faster and better to use.
However, when I connected through the Intel ports (both the Intel/Marvell ports are 6Gb/s) my boot time jumps to almost 45 seconds!
Do I need to readjust something in Win 8? I've already updated all drivers.
Also, when I run the Win Exp Index under the Marvell I only get a 7.9 for the SSD but if it's attached to the Intel I get a 8.1.
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What SATA mode are the Intel ports set to?
Try disabling the Marvell in BIOS and test again. See if the boot time is the same. Make sure that the SSD is the first boot device in BIOS.