We had an issue recently when adding a SCSI Pass-through disk to a Virtual Machine which was part of a Hyper-V Failover cluster recently.
At first we added the SCSI Pass-through disk to a VM and it was all working fine until a reboot, after this reboot the Disks were still visible however in Disk Management they were showing as RAW volumes which we knew was not the case.
We eventually found out the issues was down to us adding the SCSI controller and SCSI Pass-through disks via Hyper-V manager.
So to fix this we had to remove the SCSI adapter via Hyper-v and actually add the SCSI Controller via Failover Cluster Manager using the following steps. (http://support.microsoft.com/kb/2501763)
- In the Failover Cluster Manager snap-in, right-click the VM listed under Virtual Machine, and then click Settings.
- In the Settings dialog box, select a disk controller, and then click Add to add the disk to the disk controller. For example, click SCSI Controller, and then click Add to add the disk to the SCSI controller.
- In the Hard Drive pane, select the disk from the Physical hard disk list, and then click OK.
After these steps the volumes were presented back to our VM and we could reboot as many times as we wanted 
