Internal HDDs cannot be accessed for small intervals of time

Hello,
I have 4 internal HDDs and have had this setup for about 2 months now. I had to reformat my computer this week and have since been having a problem with my hard drives.

While I am browsing folders and occasionally even using programs, my HDDs will seize up for around 5-10 seconds. One of the drives starts to make some loading noises and then eventually they begin to work again. While this is happening I can usually use the GUI that is loaded and most things loaded into RAM, however I cannot access the HDD for anything new.

One of the internal drives was originally an external drive, the Seagate FreeAgent 500GB. I suspect it may be the culprit here. I was having this exact same problem before with it; whenever I'd plug it in through USB, even if accessing another drive, I'd have the computer seize up and have to wait for it to finish making similar sounding loading noises. Removing it from the case and plugging it in internally fixed the issue completely, until I reformatted this week.

I have checked all the cache options for the drives and they are all set the same; default which is just the top option checked off. I did this as I suspected that the Seagate drive is set with the same cache options as it did when external, but it's not the case.

I did an HDD test which writes 6 billion zeroes to three 16mb files, and then reads it... no errors on all drives.

Logically the next step would be to remove the drive and see what happens. Is there anything else I should try first? I wouldn't want to lose the drive anyways, I would be looking for a way to fix it to work internally.

Here are my specs:
i7-2600k @ 4.45
GTX 580 1.25
P8Z68 V-Pro
Win 7 64-bit

SSD1: Intel 510 128GB
HDD1: Samsung HE103SJ 1TB
HDD2: Western Digital FAEX 1TB
HDD3: Seagate FreeAgent 0.5TB
HDD4: (irrelevant as problem existed before installation)

Thanks, any help is appreciated!

Does it matter which hard drive is being accessed when the problem occurs, or is it the same with all? If all, that would suggest that the problem is on the drive holding the OS...which one is it? It is possible that the problem is software related, instead of hardware. Do you have hard drive activity lights, such as with DriveGleam or DriveLED? If so, that would pinpoint which drive is active when the problem happens. If there is a software problem, you would need to find which program or process is causing it, which you can do with the Task Manager's Resource Monitor.

Problem was the power options with the hard drives. Thanks for the help!