If you made fresh reformat after installing 3TB WD drives and Win7 still reports them as 699GB drive (
has been complained here also earlier), then my advice at the moment would be:
a) try the 1.02b03(1.13.0905.2011) FW - I know, D-Link has removed it from distribution. You can PM me, i still have it somewhere.
b) to try some other protocol than SMB/CIFS. For Windows, your options could be NFS and FTP.
I personally use similar setup (1.02b03(1.13.0905.2011) FW and 2x3TB WD in RAID1), but I connect using Mac and AFP protocol, the NAS reports itself as 2,95 TB drive.