I wasn't sure where to post this, also skip to the third paragraph to see the actual problem (the first and second are background info)
I have a Crucial M4 128GB SSD as my OS drive and its working great. Then, for storage I have a 2TB WD Black HDD, that has nothing wrong with it according to all disk health programs I have run. I have another 3TB Seagate Barracuda in an external enclosure. My motherboard (ASRock Z77 Extreme 6) is also working fine.
However, whenever I boot with an internal HDD connected (I have tried both the WD and the Seagate and on different SATA ports) the POST is not instant like when only the SSD is connected. Having my optical drive connected makes no difference.
I have disabled the splash screen in the BIOS and I see that with only the SSD all the info comes up instantly, whereas with an HDD attached it takes up to ten seconds to POST (longer than Windows' loading time!)