MSA1500cs Multipath SAN Boot and controller failover

[Don Levinson]

I have my san connected as the attached picture shows. Whenever the MSA1500cs fails to the second controller (which happens sometimes when we hot add or remove an unused hard drive) I can no longer SAN boot. But if I then go through all my blades and disable BIOS on the first qlogic HBA so that BIOS only looks on the second HBA for the boot disk they work fine. Then when the MSA fails back to the first controller I have to go and reenable BIOS on all the first qlogic HBA's in the BL35 blades. Do I need to upgrade my switches to full fabric and cross-link them? or is this some issue with the dual controller and dual FC interface on the MSA1500cs?
I cannot upgrade the MSA to active/active firmware because there are both windows and linux (vmware) servers on it.
I get the exact same results in Linux and Longhorn so it is probably an infrastructure or BIOS issue.
My other thought was that maybe zoning would prevent the primary HBA from seeing the LUN when the primary MSA controller is on standby. There is no zoning currently just SSP.

Versions:
MSA1500 Firmware Revision: 5.02b407 (SGA0614026)
MSA1500 Hardware Revision: a [AutoRev: 0x010000]
Fibre Module AutoRev: 0x020000
SCSI I/O Module Bus 0 Revision: 2.02
SCSI I/O Module Bus 1 Revision: 2.02
SCSI I/O Module Bus 2 Revision: <>
SCSI I/O Module Bus 3 Revision: <>
Fan Control Module A Revision: 2.38
Fan Control Module B Revision: 2.38
Box 1 PROLIANT 4LEE Rev: CP20 (MC3DLMPX6C)
Box 2 PROLIANT 4LEE Rev: CP20 (MBW5LMPX6C)

BL35p bios A03 3/1/2006
qlogic firmware 3.03.01
qlogic rom bios 1.45