Have you tried to run Windows without those fiber channel cards being connected to see if that makes a difference?
Hello Guys,  I have a problem with installation new system on R900. Its takes about 3-4 hours.After installation system performance is very low. OS is installed on RAID 1 (Perc 6/i) but by Qlogic card i have connected 100 another disks which I cane view on installation screen. I try to install another system, but is the same. I delete RAID and then create RAID 1 - still the same.I used SUUB, but without success. Has anyone has simillar problem? Before this installation ws2k8r2 Ent core was installed and everything was ok. Thanks for help,Martin 
Very slow installation Windows Server 2008 on PowerEdge R900