This isn't the first time I've had this problem and the last time I had it, I didn't note down how I fixed it. I just spent the last hour or so looking for solutions to this online and to my surprise, nowhere actually has an answer.
My external hard drive would randomly disconnect for just under a second then reconnect. When searching online, I found someone suggesting that the USB port doesn't have enough power to it to power the hard drive and suggested unplugging all non-essential USB devices. I didn't think it would solve it but I tried it anyway but to no avail. Here's the things I've tried:
-remove the hard drive from the device manager so Windows re-installs the drivers
-unplugging all USB items besides the HDD so no other USB items were plugged in.
-tried different USB ports
-tried the HDD on different computers (it works on others with no problems)
-looked for a powersave setting to make sure Windows isn't turning it off due to inactivity (couldn't find any option for it)
This is quite annoying as I'm trying to watch some of my old home videos I have saved on it and it keeps disconnecting in the middle of one.
Windows XP Pro SP2
Freecom 250GB External Hard Drive (not sure of specific model number. Bought in 2005)
I doubt it's the USB ports because anything else I try in them works fine.
I think that the PSU is the likely thing although the hard drive does work fine with other computers using a weaker power supply but it could be that mine has degraded. When I get the chance, I'll try replacing the PSU. I really do need a new computer though so I might just hold out until then.
In that case I am not sure, those drive don't have this problem.
Can you do a small test, Try downloading Ubuntu from http://www.ubuntu.com and run it live from CD. it will load a virtual OS running from your CD, from here plug in your drive this should verify if your problem is hardware or software.
The problem with Linux (and Mac) not being able to mount it has been there since the beginning. I remember it saying in the manual for the hard drive that it was only tested on Windows and may not work on other operating systems so that's expected.
I also tried on some non-live versions: Fedora Core 8 and Ubuntu.
I can see why you've come to that conclusion and I did too at first before I did tests. I think the reason the drive doesn't mount on anything other than Windows is because of the hidden partition it has.
Then un-hide it. But frankly, I don't see how that could affect Windows or Linuxes. It's just a bit set... the OS doesn't often care too much about the actual position of stuff on the disk, that is the job of the local controller - the OS wants to be able to understand the format and read the partition tables, and the partition MFTs, and make/accept requests of the drive, is all.
Anyway... could it be an interrupt priority problem? Does any other ext hdd behave the same way when doing the same task? Have you checked the tables for errors?