Missing/corrupted folders on external drive?

Here's the situation: My Retina MBP is my main computer and I use it to do all my downloading (movies, music, pictures, etc) but the downloaded files are always stored on an external Samsung hard drive. A few days ago, I thought I'd organize my files a bit by moving certain folders containing movies I have yet to watch, music I have yet to listen to, and stuff like that, to a separate new folder. Everything is done fine on the Mac and even when I switch to boot camped Windows 8 to check the status of my drive, the newly created folders are there with all the subfolders I've just moved into them, intact.

The problem came when I unplugged my external drive from this MBP and hooked it up to another laptop, an Acer Aspire that runs Windows 7, to access my files there. The first time I accessed the drive, I noticed that the changes I made to those folders earlier on my Mac seem to have become "undone" when I view them on the Acer. For example, all the subfolders and files I'd moved from, say, folder A, and put into the new folder (folder B) don't show up in B. In fact, the new B folder I'd just created earlier didn't seem to exist and wasn't even showing up on the hard drive, while all the files I'd moved to it were back in their original folder A. I found this odd, but just dismissed it as a temporary error, maybe due to the fact that the changes were made on a MBP using OS X and now I'm trying to view it on a non-boot camped Windows 7. Mind you, I'd moved my files to a new folder by just dragging them and holding down "cmd", so effectively cutting and pasting them.

Anyway, later on, I took my hard drive back to my MBP and surely all the files were in their right place. Folder B was back and folder A no longer contained my B files, as I'd seen earlier on the Acer. Today I checked again, and noticed that some of my files in B seem to have a duplicate copy in A. The files from both folders had identical names, and even when you try to move them to Trash, they show up as separate folders, meaning that one set of them weren't "phantom" files or anything. So I did what anyone would do and deleted the duplicates - I have no need for two copies of the same movie, song, picture, etc. on the same hard drive. Plugged in the drive to the Acer again, and this time, half of the files/folders in B were now "corrupted and unreadable" according to Windows 7. I went back to my MBP and checked the drive again - those very same corrupted and unreadable files now no longer show up in Finder, confirming my fear that they really are unreadable and unplayable, which is why Finder won't even display them.

To cut to the chase, I tried to organize my files and folders on my external drive through cutting and pasting. After taking the drive back and forth between my MBP and Acer with Windows 7, some of those files are now corrupt and I more or less have to redownload all the stuff I took so long to get.

Why is this? I'm now terrified of moving files around on my external drive. I always thought that if cut/copy/paste/rename/whatever a file on an external drive or USB pen drive through one computer, the changes would be reflected on that same drive when you access it using a different computer. This is the first time I've run into such a bizarre problem and I don't even understand why. I realize that the MBP/OS X isn't the only part of the problem, and I'm guessing something went wrong because I used two operating systems at the same time to modify and read my drive. Not sure. Does anyone know? Is there a fix for this?