Slow random I/O performance in Windows 2008 R2 with Qlogic 2560

We have a server with 2x Qlogic QLE 2560 8-Gb fibre NIC's connected to a IBM DS8700 SAN and are having some performance issues in Windows 2008 R2, specifically with random I/O

These servers were running Windows 2003 SP2 and getting good random i/o performance. We measured this with IOMeter & CrystalDiskMark

This server was migrated to windows 2008 r2 (clean install) and the random i/o performance and latency dropped by 60%-80%. The performance of our application is impacted due to this.

We have installed the latest firmware and windows drivers and checked this several times.

Any ideas on how to troubleshoot this issue?