SATA_1 Works with 3Tb drive but NOT with a 4Tb drive. and setting up LSI Raid PCI card

I have a  Dell Precision Workstation 690 with Win7-64 Ultimate installed.  In a previous posting I was told

"The onboard SAS controller that comes with the Precision 690 is called: LSI 1068 PCI-X - 3 Gb/s SAS Controller. It's pretty old at this point and I'm pretty sure it only supports MBR ( 2TB MAX limit )."

Since I did not get this reply until I had received the 3Tb drive, I tried to use the 3Tb drive anyway.

I connected the 3Tb drive to  one of the SATA connectors (SATA_0, SATA_1, SATA_2)  (not the HDD connections on the motherboard) after boot up Win7 "install drivers" for the new HD and all worked.  The computer saw the 3Tb drive (2.73Tb) correctly and everything appears to works. I currently has 2.4Tb of data on the 3Tb drive.

I then remove the 3Tb drive and installed a 4Tb drive in the same connection. The computer only see about 2.12Tb (?) on the 4Tb drive.

What is happening ???   I do not understand.  Can someone educate me. 

2.  I purchased a LSI Logic SER523 Rev B2 4 Port SATA PCI-X Raid Card.  I wanted to only use the 4Tb HD as a single drive not in a Raid configuration.  Can  someone point me to a simple how-to instruction.  I attempted to read the LSI users guide and it got way to complicated for me.

Thanks