4096 byte sector Drives vs 512 byte Drives and Partition Map integrity

I have a late 2008 Mac Pro, and every so often, if I don't take the time to Defragment my startup drive, or go over it with Disk Warrior, my partition takes a dump. Normally its a invalid file count, invalid directory count, invalid volume structure, or some combination in between. I don't think its the drive or the mac itself (at work we have 200+ macs of various years and models that do this too) since it only happens to the startup drive (1TB-56% full) and I've had apple replace them 2 times now, along with a replacement machine and it still happens. I was wondering if the GUID would be happier on a new 4096 byte sector drive assuming the mac would even be able to use it. Buried deep in the developer site is a tec note that says Mac OS 10.4 and up are able to use the drive, but I haven't been able to find out if anyone outside of Western Digital has actually used them on a mac yet. No one at AppleCare seems to have an answer to my question, or can explain why my map fails regardless of drive.

http://developer.apple.com/mac/library/technotes/tn2006/tn2166.html