I want to use an PCIe SATA Controller for EXSi and a virtual Storage VM (Napp-it). The onBoard SATA Controller should connected with VMDirectPath to the virtual Storage VM. With ESXI 4.1 this works fine with an an patched (JMicron JMB361 PATA Support) ESXI booted from an USB Stick and the Storage VM on an onboard PATA Drive.

In ESXi there is now no Driver for my jmicron Pata controler so i try something new.

I installed ESXi 5 on a SATA HDD connected to an PCIe Marvel SATA Controller inserted in an PCIe Slot. It works for the ESXi boot and i can use the SATA HDD as a storage for VMs.

Then i changed the onboard SATA Controller (AMD SB850) of my mobo (ASUS M4A89TD Pro/USB3) to VMDirectPath. After reboot the SATA HDD connectet to the extra Marvel SATA COntroller are no longer visible as a storage.

What connection is there between the onboard sata controller and the extra marvel sata controller??? Why i can´t use the VMDirectPath for the onboard device without efects to the PCIe SATA Controller?

Wirrkopf you are not alone, I have a similar problem with my Asus P6T Deluxe V2 mobo, when I enable VMDirectPath for the onboard Intel ICH10R SATA controller and then reboot, the onboard Marvell 88SE6111 SATA/PATA controller also gets removed from ESXi Storage.

i want to do the similar things.
i need a sata pcie 1x card for esxi boot and VM datastore in the HDD. after that use IOMMU to pass-through the southbridge 6 SATA3 HDDs to the VM to make a ZFS raidz1.

Hardware: AMD Asrock 990FX extreme3 990FX + SB950 ( support IOMMU of course)
PCIe 1X + 2 PCIe 16X + PCIe 4X
image that will happens .....
first PCIe 1X :sata contorller card with esxi and NAS-VM-System on a HDD
2 PCIe 16X :passthrough 2 VGA card in 2 different VMs
last PCI-e 4X : dual ports internet card such as 82576/bcm5709 passthrough to 2 different VMs

is it possible?

Are you able to post a screen shot of the VMdirectpath configuration screen?

For a case such as this, are the two devices on the same PCI bus?

"when I enable VMDirectPath for the onboard Intel ICH10R SATA controller and then reboot, the onboard Marvell 88SE6111 SATA/PATA controller also gets removed from ESXi Storage."

I faced the same issue.
Motherboard: Asrock B75 Pro3-M
Onboard SATA: Intel + Asmedia 1061 SATA3
After pass-through the Intel SATA controller, the Asmedia was gone as well.