I'm having a really strange problem; I have 3 hard drives, all of which seem to work:
1. Corsair Force GT 120gig SSD, sata 3; OS installed on it; set to priority #1 in bios boot loader
2. OCZ Octane OCT1 128gig SSD, sata 2
3. Western Digital Caviar Black 500gig sata 2 (I think sata 2, anyway, it's older)
When I have only the 2 SSDs (#1 and #2) plugged in, the computer boots incredibly quickly, finishing loading before the windows animation has time to complete.
When I have all 3 HDs plugged in, windows takes *forever* to load, which is really strange, because no OS is installed on the 500gig (and it's not part of the boot order). When windows finally boots, HD #2 isn't detected and windows allocates the D: drive letter to HD #3. I tried setting the drive letter on HD #3 to F:, to see if that was causing the conflict, but there was no changed in behavior.
It seems like it has to be a windows issue because it takes so much longer for it to load, but I don't think all 3 HDs were detected in the bios (though I'm going to check as soon as I'm done writing this; and I feel dumb for not checking for sure ahead of posting).
My motherboard is a ASRock Z75 Pro3.
All 3 HDs can write and read data when they're detected.
Your title and your content seem to be different. Are you experiencing a problem where plugging in your third HD causes one of them to not register, or are you experiencing a problem where plugging in your third HD causes slow boot times? Those are two very different problems. Either way, as a precautionary measure I'd double-check the disk using any program you'd like (chkdsk even) to ensure the 500 gig doesn't have bad sectors. Also, just a miscellaneous question, did you properly align your SSDs when you installed them?
Both issues (slowdown and non-detection) occur when all 3 HDs are plugged in; that is to say windows boots slow AND HD #2 isn't detected. There have not been any cases where one symptom occurs in the absence of the other. The title field didn't allow enough characters to explain both. Removing HD #3 (which doesn't have an OS on it) causes windows to boot more quickly. I am aware that this doesn't make sense.
On one instance so far, all 3 HDs were plugged in, detected, and windows booted quickly.
However, the slowdown of the 120gig drive #1 and the non-detection of the 128gig #2 drive only occurs when the 500gig is plugged in. There has been no slowdown or non-detection while the 500gig is unplugged.
My system drive (120gig SSD, #1) is misaligned. My extra SSD (128gig SSD, #2) is properly aligned. But this causes write speed to decrease, not read speed.
Sure - I wasn't attempting to insinuate that the misalignment may be a catalyst of the speed reduction, I was simply suggesting you check something that I've commonly seen others fall victim to.
One diagnostic technique I would advise you to try is unplugging the extra SSD (whichever is not hosting the OS) and then plug in the 500gig and boot. Do you still see a slowdown similar to when the extra SSD was plugged in? If so, we can assume this problem is being caused by the presence of the 500gig. If the slowdown is not present with two drives, the problem may be located elsewhere such as in the motherboard having a problem dealing with whatever number of devices are utilizing SATA slots at that time, or even the individual SATA slot itself.
Did you end up running any type of diagnostic tool on the third drive, the 500gig? Checking that the 500gig is healthy (no bad sectors) can ensure that the problem you're experiencing isn't the result of some frivolous attempt by the system to compensate for one of the 500gig's shortcomings.
P.S. - One other thing about misaligned SSDs is that they are being forced to do more work, and as a result the life of the device will be dramatically reduced. You may want to follow the guide I posted before and properly align your misaligned SSD to extend its longevity.