  It's not odd. Windows cannot use a "disk" larger than 2TB unless the disk is formatted as GPT. Windows cannot boot to a GPT disk unless Windows is installed on UEFI-enabled system. The 2900 does not support UEFI, so you MUST have a "disk" configured smaller than 2TB for the OS. You can do this by splitting up your disks (2x1TB RAID 1 for OS, 3x1TB RAID 5 for data) or "slicing" (create one VD of 200GB for the OS, one VD of 3.8TB for data). So, since the machine is only BIOS capable, Windows can't convert your 3.4TB disk to GPT to support a size larger than 2TB.   If your firmware is out of date, you may never be able to install the OS, as the built-in drivers for the PERC may require a minimum firmware level on the PERC to operate. You can use SMTD/SUU, Repository Manager (linux packages to create bootable ISO), or install an older OS and update the firmware manually/individually then install 2012.
I have a PowerEdge 1900 originally running server 2003. I have 6 brand new, initialized, 750gb hdds in a raid 5 array. I'm currently trying to do a clean, first time install of Server 2012 R2 and 28% into the install I get an "driver irql_less_or_not_equal megasas.sys" error. I cannot figure this out. I'm desperate for help. This is my first server setup by myself. 
Dell PowerEdge 1900 Perc5i Raid 5 HELP!