Probably because the 3ware card is doing some funky RAID (i.e. non-HBA only) stuff. Or that the controller doesn't support drives over 2TB.
Any source for that? AFAIK, my 9650SE supports JBOD mode, in which it just acts as a SATA controller.The 9650 should not be used, period. It has no true JBOD mode.
I had that card... bought it and sold it 2 months later when i realized it is totally not even close to what you really "need" from your HBA controller.
[root@freenas ~]# camcontrol devlist
<AMCC 9650SE-12M DISK 4.10> at scbus0 target 0 lun 0 (da0,pass0)
<AMCC 9650SE-12M DISK 4.10> at scbus0 target 1 lun 0 (da1,pass1)
<AMCC 9650SE-12M DISK 4.10> at scbus0 target 2 lun 0 (da2,pass2)
<ST980811AS 3.CDE> at scbus3 target 0 lun 0 (ada0,pass3)