Motherboard isn't recognising Harddrive bays

To starts, my set up specs are;

Mobo - Z87 GA45 Gaming (brand new)

CPU - i5 4670k (brand new)

Ram - 8GB Gskill 1600, 8GB Geil Cobra 1600

Storage- 2TB Seagate 7200rpm HDD, 250GB Samsung EVO SSD

PSU - Antec 850W Signature

Case - LianLi Tyr PCX2000

OS - Windows 7

I bought the i5 second hand, but still unused a few weeks ago at a very good price, but of course needed a new mobo to accomodate it, since I was using an older GAX58-UD4P with an i7 920.

Hooked it all up, everything seems to be working apart from the hard drives. The case has 6 hard drive bays that are hot swappable, although I never move them. I have connected the HDD to the power supply and to the mobo correctly. The HDD is spinning up on start up, so it's getting power. However the mobo doesn't recognise that theyre even plugged in.

My cables all work, I plugged into the HDD directly and it recognised straight away with the same cables. I've also tried multiple hard drive bays, all to no avail.

It was suggest I turn on AHCI in the bios, this was already on however. I did put it on IDE mode (no idea what it is tbh) and it did recognise one of the HDD, although it couldn't read any data off it.

I have this posted on the MSI forum also, things we've ruled out -

My ram is not causing any troubles.
It's booting in legacy+UEFI mode.
It's set to AHCI Sata mode
The 2tb HDD does have my old OS on it, it should still get recognised. Whether it boots or not is the question. As of now I can't even format it.
My brand new SSD isn't recognised either.
Running in IDE mode isn't actually helping, windows says it's unable to format the SSD and won't find the HDD