What version of Mobipocket Desktop are you using? Version 6.0 will move stuff and put it in the "documents" folder, 6.1 and 6.2 will not.
I don't use it, but MobiDesktop is a pretty good piece of software. It will sync your ebooks between your Kindle, PC, and whatever other Mobipocket device you have. Plus, it also has a huge offering of RSS feeds that can be generated into ebooks and moved automatically to your Kindle.
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