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[ubuntu] lzma archive has lost it's folder hierarchy?

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http://ubuntuforums.org – So I rescued files off of a computer, put it in an encrypted zip archive. The zip archive is 32 gb's. When I run a test on it, the contents are listed correctly in their subfolders, however if I actually extract it into a clean empty directory, eventually it prompts me asking if I want to overwrite a file is already there, I opted to rename the files automatically and it proceeded to spew every.single.file on the top level directory, as well as every.single.folder on the top level directory, each folder is empty. I'm at a complete loss as to what is going on here, is there a way to restore th (Hardware)