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I'm using KDE 4, but I believe this issue happens regardless of desktop environment. File copy dialogs say that they're done, usually in just a few seconds, but the USB drive keeps writing for minutes afterward. The kind of files I'm copying are large (300 MiB+), so I'm wondering why the dialog thinks that everything has been written when it in fact has not.
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Maybe this is because of the write buffer?
Try mounting the media using the -o sync option to have data written immediately.
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