External HD not staying connected

I am really going crazy trying to figure out why my 1TB Western Digital keeps disconnecting from the computer.
First off I am running USB 2.0 and the external enclosure is a 3.0 with eSATA, I do not use eSATA but it's there just in case. After loading it would stay connected for about a minute or two after Windows went to desktop then it would disconnect. I tried switching USB ports, I tried using a different cable, I've tried disconnecting and re connecting the cables but nothing worked, I even run WDDiag on the drive, not the extensive test but the quick test and the drive passed. I could shut down the enclosure after it disconnected and then turn it back on and it would connect. Normally my external hard drives start when my computer starts as they are connected to my Battery Backup. I even shut the drives down and let Windows load first then would turn them on and that didn't do any good.
Thinking there might be something wrong with the External Enclosure I did an RMA and I received my new enclosure. I again inserted the 1TB Western Digital and again the same thing started happening as before.Then I did some more reading and found DriveCleanup.exe, so I ran the exe and it seemed to work, the drive was running fine. I shut the computer down as I had some things to do and came back and fired the computer up. After getting to desktop I noticed that Windows was installing a driver, for what I have no idea, after the driver was installed I lost the hard drive again. I ran DriveCleanup.exe again and this time rather than using the 3.0 enclosure I put the 1TB WD into a 2.0 enclosure and I have no problems with it. The funny thing is I'm running a 3.0 enclosure, witout eSATA, with a 500gig WD and never had a problem and I've been running it for about a year.
So if my 2.0 works, why say anything at all. Well, after going through hell with this thing, I want to know what could be the problem. Any help would be greatly appreciated.

OS - Windows 7 Ultimate wit all updates current
CPU - Intel i7 860
Graphics - EVGA 680
Memory - 16gig Corsair
PWS - Kingwin ABT 1000MA1S
MB - EVGA P55 200 Classified

Update - Contacted WD and talked to a Tech Rep. He told me to run an extensive test on the drive and see what happens, the disk is still under warranty so if any problems they will replace the drive. After running for about 8.5 hrs the test finally finished with no errors. So that's very interesting. Now to talk to Microsoft about the drivers for the USB. I dpubt if I'll get anywhere but at least I'm going to try.

The enclosure is made by Rosewill and it's model RX-358 U3C. I've been using Rosewill for years and never had any issues. The HD is made by Western Digital Model WD1002FAEX Black. I have a WD VelociRaptor 1TB as my primary and love it. The reason why I have my drives connected to my Battery Backup is because I have a transformer right outside my house so I'm the first to receive power and I have noticed that the power does fluctuate and sometimes there are surges, not much but enough to make me cautious. One time the transformer decided to blow up. I can imagine what could happen if the transformer was hit by lightning. So, I'd rather be safe than sorry. Everything in my house that has anything to do with electronics are connected to surge protectors to include mu Central Air, paid a couple bucks for that thing. Anyway I'm going to try something else, don't know if it'll work but I'll try anything once, sure can't hurt. Will let you know what happens.