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Does it work when you run it from a console?
I start unclutter with a link in my kde autostart folder and it works perfectly. Perhaps you can try something similar with your desktop environment, whatever it is*. Also, unclutter has a large number of options, some of which are workarounds for when something keeps it from functioning. Read the man page and try some of them out.
*(You really should mention things like what distro and DE you're using when you post things like this. Try adding them to your permanent profile.)
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Unclutter in .xinitrc does not seem to run.
