Probably not your problem, but one sign that a drive is about to die is if it starts working noticably slower, especially in file-copy operations (both to and from the drive). I had this happen with one of my drives, at first I thought it seemed slower when copying a show to it, but didn't really think anything of it, until after a while I noticed that all file copying with it was going so slow, and that other drives were still fine. After a few more weeks, it died altogether.
Besides using something like chkdsk, you could try doing other file copy operations to it a lot and see if you get any errors. You could also try loading a bunch of torrents onto it, mainly 3-4gb dvd torrents, and see if any errors come up while downloading them, since torrents use constant writing over a longer period of time. If any of those things happen then it's a sure sign the drive is dying and has problems. The fact that it seems fine with linux, I have no idea. Other than that, I can't help, but good luck.