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ELFswe: The problem seems to be that Galaxy don't have permission to download to the root of my drives. But it can download to subfolders.
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rtcvb32: If you go to properties, then security, there's a list of users of each folder. If malformed it will cause folders not to be written to. Otherwise as administrator you can add or modify the appropriate user to have full or read/write access.

I've noticed using tar to make and extract archives can make malformed data in Cygwin... So...
Late reply......

I'm only having this problem with Galaxy. Other softwares can write to the root folder.