1 TB Caviar Green 64 MB Cache (WD10EARS)

WD Internal Drives Desktop & Mobile Drives
21

I have no experience with your setup, but AFAICS there should be no problem running your system as it is. All it means is that you have 1MB of wasted space at the beginning of each partition. I believe that your partitioning software is being confused by the 2048 sector offset because it normally expects to see only a 63 sector offset. IMHO, there is no actual problem.