External hard drive does not show some (sub)folders, but recovery software shows that they are there

Hello experts!  I have and external Lacie 250GB hard drive (NTFS, 1 partition), with all kinds of stuff on it.  I use it every day, and frequently move it from computer to computer.  Today I noticed that I am missing some subfolders in my music directory.  The whole drive is backed up, so I checked the backup, and the files are indeed there.  I ran PC Inspector File Recovery (awesome freeware program), and it shows all of the folders and files in tact, exactly how they were.  I have tried the drive on two different computers, and they show the same problem.  I'm guessing the problem has to do with XP.  Sometimes my laptop refuses to allow me to "remove" (via system tray) the external drive, so I just turn off the drive and unplug it.  I am guessing windows doesn't like this and maybe has jacked up the MFT.  I have the drive set to "optimize for quick removal", and yes, I have scanned the disk, restarted the computer, and have anti-virus software.

My questions are these:  Is the drive going bad, or is part of it bad?  Is there a quick fix besides copying from the backup?  What the Bleep am I doing wrong to deserve this (in terms of computer use, not ethics and karma)?