External HD (Seagate GoFlex) not always detected by Windows

I've got a few different external hard drives - two are portable (as in USB powered) and as such are often moved between my two computers, or taken to work, etc. and back. My third is a mains powered external hard drive, a 2tb USB 3.0 Seagate FreeAgent GoFlex Desk, that's used for backing up and just stays permanently on my desk (and has done since I bought it).

However, I've had an issue with this Seagate GoFlex drive since I bought it - it doesn't always show up in Windows. When I boot my PC, if I have either of the portable drives connected, they are visible in My Computer right away (and in fact Autorun pops up, so I know they're there). But that doesn't happen with the GoFlex. I have to either disconnect and reconnect the USB cable or the power cable for it to be detected by Windows.

Once it's been detected, it tends to stay connected - there were a couple of times when it disconnected on me, once even during a file transfer, but mostly it's there and reliable until I next come to use my computer, only to find it doesn't automatically connect again.

I assumed this was some sort of power saving feature, so I looked into it and found that you can change drive settings using software called Seagate Dashboard. However, after installing this software I found that my drive's sleep time was already set to 'Never' rather than the default of '15 mins', and even after double checking that it's 'Never' I'm still having this problem.

I would actually like my drive to power off after 15-30 minutes, to save power and preserve drive life, because it's a backup and I don't need to access it that often. But I would like it to 'wake up' and be there when I need it.

What could the problem be? Any other settings I could try (and where are they)? Or could it be a faulty drive, or a faulty motherboard/USB controller? (I've tried it in all of the USB 3.0 ports I have.)

Is it that serious? Should it not be behaving like this at all?

Yeah, I can live with having to re-plug it - it's always on my desk, so it's minimum effort for me to reach over to it. But if it's not supposed to be behaving like this, is that cause for concern? Like a symptom of a bigger problem that could ultimately lead to data loss?

I've checked for new drivers. My mobo ones are up to date (it's an Asus P8Z68-V Pro and the latest driver was already out when I bought it, so that's what I'm using). I'm not 100% sure about the drive - it's difficult to get a read on it with it being in an enclosure, for example HD Tune gives its name as Seagate FreeAgent GoFlex Desk Drive, rather than the actual model number of the drive inside, which I thought was a Seagate Barracuda Green ST2000DL003-9VT166, but the Seagate website says the latest firmware for that drive is CC32 whereas HD Tune says its on CC98. So either I've got the wrong model number or Seagates numbering system makes no sense. Either way, I don't want to attempt updating the drive's firmware until I can backup everything on it, and I currently don't have enough space for that on any other drive - I'll borrow another one from somewhere so that I can update the firmware on this one and/or return it to the store. I only bought it in June so plenty of warranty left.

In the meantime I'm going to switch to using it on my laptop, to see if the same problem happens on a different computer.

Okay, so this is interesting - this problem doesn't occur with my laptop. I tried connecting the GoFlex Desk to my laptop - the hard drive was plugged into the mains, the USB cable was just loose on my desk and hadn't been plugged into anything for at least 48 hours, the laptop was completely powered down. I powered on my laptop and, as Windows booted, I heard the drive spin up and an LED came on, then started flickering. When Windows was booted, I went into My Computer and the external hard drive was present.

This is the behaviour I want and would expect from an external hard drive. As it works with my laptop but not my desktop, I suppose that means the issue lies with the desktop somewhere - although I don't have this problem with my two USB 2.0 drives, even when connected to USB 3.0 ports.

I have another quick question at this point - if I reactivated the power saving feature on this drive and set it to power down, say, after 15 minutes - would it still be visible in My Computer, and just take a few seconds to spin up again when I click on it?