My Iomega 500 NAS was having trouble deleting some .iso files even as root! the fix was to use gparted to check the file system after unmounting it.
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<p>GParted 0.4.8</p>
<p>Libparted 1.8.8.git-dirty</p>
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<b>Check and repair file system (fat32) on /dev/sdb1</b> 00:06:20 ( SUCCESS )
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calibrate /dev/sdb1 00:00:00 ( SUCCESS )
etc........................