Really odd problem with WD2002FAEX in MacPro 5,1 mid 2010

Hi all,

Please help.

Current configuration:

Mac Pro 5,1 mid 2010

16GB (4X4GB) memory

Both optical drive bays loaded one Superdrive, one LG Blu-ray burner

One external NewerTech Guardian MAXimus connected FW800

All 4 internal drive bays filled with Western Digital 2TB WD20EARS

Bay 1 - boot

Bay 2 - time machine backup

Bay 3 - itunes

Bay 4 - time machine backup

Problem: initially interested in replacing iTunes drive and boot drive. SATA II drives look to be going the way of the dinosaur. They are starting to get a bit hard to find. Every site seems to state the SATA III drives are backward compatible to SATA II. ok. Here's the problem: When I swap the drive in Bay 3 with the new WD2002FAEX drive, on spin-up I lose my USB ports and Airport card. All communication stops. Thinking it was the drive, I returned it to Newegg. Purchased same drive at OWC. Installed drive, same result. Thinking it was Bay 3, I used another. Same result. Thinking it was the model of drive, I purchased a Seagate Barracuda ST3000DM001. Put drive in Bay 3, same problem. I retained the original drive that came with Mac Pro, Western Digital Caviar Black WD1001FALS, put it in, works OK. I'm thinking it's SATA III, but I've searched all over, and I can't find anyone else who has had this problem. Each time I take the SATA III drives out, my USB ports and Airport card return to normal like nothing happened. Also, when I have the SATA III drives in, it seems to take longer to boot up.

Any ideas?