First, your configuration is playing "fast and loose" with MBR data structures. MBR is generally considered to be limited to 2TiB disks, but in fact it's limited to 2TiB values for partition start points and sizes, so it can theoretically handle just under 4TiB disks, albeit with the final 2TiB in one partition. On your 3TB (2.7TiB) disk, your largest and final partition is about 1TiB in size and begins at about 1.7TiB. It therefore is within the letter of the MBR "law," but some OSes and utilities will flake out when shown this disk. In my tests, both Linux and Windows 7 handled this configuration OK, but most other OSes didn't. My tests were limited, though; it's conceivable that some utility would fail on this disk, even under Linux or Windows 7, and possibly corrupt your data. In fact, my guess is that this is what's happening to GRUB, although I'm not positive of that. Overall, I'd have to recommend the use of GPT on bigger disks.
That said, I realize you may be in trouble if you're trying to use a 3TB disk on an older computer with a traditional BIOS rather than an EFI. In such a case, the best option is to use an older and smaller disk as a Windows boot disk along with a secondary GPT disk to hold data, programs, and Linux. Another option is to use DUET or Clover to get the BIOS-based computer booting in EFI mode. Both DUET and Clover can be thought of as BIOS boot loaders that add EFI capabilities to a BIOS computer. Unfortunately, neither of them is easy to install, and the last time I checked, both had problems on most AMD computers. (They're more likely to work on Intel-based systems.)
I'm not positive, but my suspicion is that the problem you're encountering is due to the fact that your boot partition extends beyond the end of the hard disk. Thus, if you really must get this working as-is, my recommendation is to rearrange your partitions so that both the Linux and Windows boot partitions reside entirely under the 2TiB mark. Use the space beyond that point for a data or programs partition.
If your motherboard supports EFI-mode booting, a better option is to switch to GPT and boot in EFI mode. This page covers converting Windows to boot in EFI mode. Linux tends to be a bit easier; you need only install any of several EFI boot loaders for Linux. GRUB 2 is one of these, although rEFInd is likely to be easier to install manually. Note that most computers sold since mid-2011 use EFI, although most sold prior to the release of Windows 8 booted in BIOS mode by default. Even some pre-2011 computers support EFI-mode booting.