NTFS works fine with GPT   its Legacy MBR that doesnt work with 4TB partitions.  You have to be set to AHCI to get GPT to work.   INTEL RST Raid does not support larger than 2TB partitions.  Booting larger than 2TB also requires 64 bit os.

http://www.seagate.com/support/downloads/beyond-2tb/

Quick facts about Windows and 3TB drives:

• Windows 10/8/8.1/7 and Vista support GPT 3TB single partitions
• Windows 10/8/8.1/7 and Vista can only boot GPT on systems with UEFI BIOS
• Windows 10/8/8.1/7 and Vista can mount a GPT non-booting data drive
• Intel RST device drivers before v10.1 do not support 3TB disk drives
• Windows systems with Legacy BIOS and MBR boot drives are limited to 2.2TB partitions
• Windows XP does not support GPT
• Windows XP sees a 3TB drive as 800GB on boot or data drives
• DiscWizard software can install a device driver which opens the full capacity of a 3TB. You can use it to create a second partition for the capacity above 2.2TB 

Version of Windows? And how are the 4T drives formatted, NTSF or GPT?

Does BIOS support GPT HDD formatting which is needed for drives >2 GB, the limit for NTSF drives?

You can get around that NTSF limit by making sure the cluster size is larger than the minimum size of 512 bytes, or by creating separate partitions on the HDD, each with a different drive letter, that are no larger than 2 GB.

Sorry for not giving all the details before.

It's Windows 7 64bit Enterprise.

Drive was initialized with GPT and then was formatted as single NTFS partition. 

The system does see entire drive.

I don't really know what BIOS supports, so where can I find out about it?

I'll try to increase the cluster size.

Yes, I set the system to AHCI and GPT. I'm not trying to boot from that drive.

I'll try first the smaller cluster size and if that doesn't help I'll divide the disk on 2 partitions.

With Drives larger than 2TB you must use larger physical sector sizes called Advanced Format. The default sector size has been 512 bytes since the advent of the personal computer. Advanced Format sectors are also called 4K sectors, because each physical sector now holds 4096 bytes.

While the physical size is 4K, the disk drive processor presents the data over the cables to the computer as ordinary 512 byte sectors.
This is called 512 byte emulation, or 512e.

The operating system will run slightly faster if it is "aligned" to the Advanced Format hard drive. Reading data from aligned or misaligned drives is the same. Writing data to a misaligned drive is slightly slower. Reading data accounts for the great majority of disk drive usage. During setup, Windows 7 detects Advanced Format disk drives and adjusts the partitions automatically for alignment;

Windows XP does not.
Linux distributions based on the 2.6.34 kernel provide full support for
Advanced Format 4K Sector disk drives.
Limited support for 4K began in 2.6.31.

Unfortunately, the Intel device driver (Intel Matrix Storage Manager 8.9.0.1023) bundled with the Windows 7 Installation CD will not work with the Advanced Format Drive. Most often, the installation process asks for  other F6 drivers for use with the system configuration resulting in failed installation of Windows 7.

You must use F6 drivers with INTEL MSM / RST drivers that understand Advanced Format. Intel Rapid Storage Technology (RST) driver v9.6 and above.  For Drives larger than 2TB REQUIRE INTEL RST 10.1 and above.

http://www.intel.com/support/chipsets/imsm/sb/CS-031502.htm
http://www.intel.com/p/en_US/support/highlights/chpsts/imsm

https://support.microsoft.com/en-us/kb/982018

For disk drives beyond 2.2TB, the proper level of Intel RST F6 driver MUST be v10.1 or higher.

http://www.intel.com/p/en_US/support/highlights/sftwr-prod/imsm

 In the case of the 9020 this is Intel Rapid Storage Technology (RST) Driver version 13.2.4.1000 - Drivers for Intel SATA chipsets 7, 8 and 9 Series. Supported OS: Windows 7  32 / 64 bit

https://downloadcenter.intel.com/download/24293