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there, I am having this problem: I have 3 sata hard drives that are working perfectly on Ubuntu but on Windows 7 two of them work awful (very very often it hangs for like 2 minutes to load the contents of a folder) and the other one is not even recognized. Also, the windows 7 boot is taking ages and i think it's because of this, I am pretty lost here... any ideas? The 3 of them are ntfs. Thanks

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Are the drives fragmented? – James Young Jan 14 '13 at 0:18
    
Since Windows is booting slowly I would consider the possibility of checking for malware. I had a similar problem and it turn out I had a rootkit virus. – To Do Feb 11 '13 at 22:56

I wonder if the filesystems are slightly corrupt (or have been corrupted by Linux) and if it needs an fsck in Windows ? While NTFS is supported under Linux, its not a native filesystem.

Another possibility (but I'd imagine less likely) is something to do with Advanced Formatting/GUID and different ways of reading large drives/backward compatibility ? If your drives are > 2tb, this is worth serious exploration.

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