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There are 2 types of reboot... a "soft reboot" which happens when you hit ctrl-alt-delete or select "Reboot" from windows start button...
the other type of reboot is a "hard reboot" which is done by hitting the reset button, or switching the machine off and then back on again.
I don't think there is too much difference in this anymore, unless you are attaching new devices to your machine.
... in older machines... I mean like 5+ years old, with old operating systems, it did make a difference as it was possible that some of the programs were still holding onto resources after a soft reboot.
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