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I have set up Ubuntu 12.04 on one hard drive, and Windows 7 on another, the bootloader being on the former. After about a month of using solely Ubuntu, I tried to boot W7 and got a message on the lines of : NTFS inconsistencies detected, MFT does not match MFTmirr. Also, I was unable to mount that drive when I got back to Ubuntu. It prompted me to use scandisk or some other tools- ntfsfix did the job.

A similar problem occurred before, but with a flash drive, also in NTFS. After plugging it into a PC using Lubuntu, the flash drive becomes unusable on Windows- it just does not show up. This USB issue is not an isolated incident- I have heard the same story from a couple of people whom I know.

What could be the cause for this erratic behavior?

Edit 1: I was advised to edit my question and ask for the specifics of the drivers that handle mounting. Does anyone know how I could look inside the ntfs-3g package and make some sense of it?

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I had this problem before. In my experience, this issue is caused by not properly unmounting drives, especially the USB. This can cause inconsistencies in the file table, especially if you remove the device in the middle of a file transfer. Just be sure to right click on the drive and select "eject" when you're done with it.

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I guess I'll have to settle with this answer, even though it's not the one I was looking for. Thanks, though! –  Goran_Mandic Jul 19 '12 at 21:38
    
@Hank_Gettinger- I am sorry for my lack of StackExchange etiquette, but another user has convinced me that I should not accept answers unless they solve the problem to satisfactory degree, so I will unaccept. No hard feelings :( –  Goran_Mandic Jul 19 '12 at 22:48
    
No problem! I'll keep thinking, let me know if you come up with something else. –  Hank Gettinger Jul 21 '12 at 1:14
    
Okay, I've done a little more research on ntfsfix. I'm guessing that while you were editing files on the NTFS partition, something happened, maybe a powercycle, that caused those changes to not be written to the journal. Hence, the inconsistencies. ntfsfix resets the journal. Could you back up your partition and see if you can reproduce the error? –  Hank Gettinger Jul 21 '12 at 20:41
    
Before I've abandoned Ubuntu to give Fedora a try, I used ntfsfix, and it fixed the problem (curiously, after two tries- after the first time, the console lines told me that ntfsfix had failed to fix the MFT and MFTmirr mismatch, and after the second try, it showed none of the previous messages, but somehow got my drive working). So far, no new problems. I just wanted to find out if the origin of this bug, and possibly if it would appear in other Linux distros. I still can't accept your answer, but I can upvote it now- it DID help ;) –  Goran_Mandic Jul 22 '12 at 1:49
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