I've had similar experience with the 3ware 9650se-8lpml with both Seagate (ST3500630NS) and WD drives (WD5000YS). I lean towards the 3ware controller as the guilty party.
My performance interest is sequential reads/writes of files > 1 GB. Six WD5000YS drives produce a max of ~60 MB/sec reads for RAID-0, RAID-5, and RAID-6. Seagate drives were around 120 MB/sec for RAID-5 and RAID-6 reads. Write performance is in the expected range of 200-250 MB/sec for both HD brands.
Using the MB's own onboard Intel sata/raid chip with just 4 drives and RAID-5 yields > 200 GB/sec reads for both Seagate and WD units, and write performance is ~120 MB/sec.
The PC is plugged into a UPS, and I've got the higher performance cache enabled.
I've also seen the random drive startup problem, and my own solution has been to plug jumpers onto the WD drives' pins 3 and 4, to configure the 3 ware card to 10 sec spinup time and then configure the MB BIOS to also use a 10 sec drive power up time. Doing just the jumpers and the 3ware spinup time was not sufficient. After a whole 2 weeks, I've had zero startup failures. Before that I spent a lot of time watching drives get reconstructed. (Yes, I know the unit is usable during this reconstruction time).
Good luck to us all. I'm going to take a Halloween break from this particular headache.