RAID is driver/chipset specific Windows 2000 supports NTFS and I assume the HDDs are formatted NTFS. The 2TB/drive concerns me, while I appreciate theoretical limits - 2TB HDD weren't around in '1999'. Even the 3TB+ 'today' require BIOS fixes to run.
So running a 6TB RAID array might be the problem.
Q - have you tried to migrate the array to a 'newer' system to see if it's a Card or 'OS'/MOBO problem?
ref - http://www.siliconimage.com/support/searchresults.aspx?pid=28&cat=27Note: The maximum allowable size of a RAID group that can be created by the SATARAID5 Manager is 144,115,188,075,855,872 bytes (which represents 248 bit addressability). However, some Linux platforms may limit the maximum size of a volume to 2TB, so the largest allowable size of a RAID group is 2,199,023,255,552 bytes.