Z87 GA45 Gaming isn't recognising hard drive 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
Case - LianLi Tyr PCX2000
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.
Any ideas on what could be wrong?

Quote from: Sea Dog on 24-July-14, 15:26:12
Test outside the case on a piece of plain cardboard or untreated wood then.
It's working fine with it outside the case. Didn't even need to wipe the OS, and it's in AHCI mode. The bays worked perfectly on my old mobo, that was only in my case yesterday....I doubt all 6 have broken in this amount of time.
I'll try and download some updates for the mobo and try again. Are there any old drivers for the Gigabyte mobo that could be causing conflicts that should be deleted?
EDIT-
I have updated the mobo with everyone on the MSI updater list, it however has made no difference. I have formatted the SSD and cloned my OS partition to it, it works fine when plugged directly in, however same as before, is not detected when plugged into the hot swap hard drive bay

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