You need to format the disk in drive.... a more mysterious case

Question

This problem has almost drives me crazy. I DIY my first PC since 1993 and have never been facing such an unsolvable problem at all, without any clues!!!!

I have a DIY PC running XEON E3-1230 and a Gigabyte mother board. It works perfectly at the beginning. I used it for around 1-2 weeks then the PC was not actively in use for around 1 year.

Last year September, i switch this machine on again and using it as my day-to-day PC, then my nightmare starts. It has the following symptoms:

1. when the computer is running, one of the two Data HDD will "disconnect" from the the PC, and "reappear" after some time.
2. When plugging in an external USB HD, it will prompt the message "you need to format......", the message will keep prompting endlessly, many windows will be opened. In My Computer, i can see drive J:\ appear and disappear continuously. It happens to not just one external HDD, but also some other HDD and card readers. But it does not happen to ALL USB storage, some of them works perfectly and never have problem!!!!!!

I have tried all the scan disk, fix disk, partitioning tools.....etc, but it doesn't help. The strange part is, there are some USB device that will NEVER have such a problem!!!!! Then one day when i was desperately sitting in front of my PC, i used one of the GOOD HDD's micro USB cable, plug it to a "BAD" HDD and then to the PC's USB port.....then magic comes....it works!!!!!!! By comparing different device and cables combination, i finally figured out there are a few cable that will work!!! It's STRANGE because all the "problematic" cables work in ALL other PC, notebooks, even PS3, but not "this" PC!!!!!!!

It must be my PC's problem!!!

Then in one day, i have no further clues and start to think of the "power" issue. Maybe my USB drive don't have enough power????? OK, i bought a brand new 600W Power supply and install it...........it doesn't help (former one was 450W)!!!!

OK, then i start thinking about the Mother Board, is that the USB Controller in my MB has some kind of problem???? I bought another brand new ASUS mother board and install it. With my Windows 7 re-installed .............it doesn't help.

Next step, will it be the CPU????? I have no further clues..............

Any expert here can give me further clues, i have really scratched my head to bleed and have no further idea!!! Is that a hardware problem? software problem?

May god help me.