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What do you mean "restarts"? The whole server reboots? Some service? Webmin?
Nothing Virtualmin sets up during installation would cause this. Perhaps you have hardware or kernel level problems that are triggered by the nightly cronjobs? (The nightly cronjobs are usually the hardest work a server does each day, and so can exercise problems that don't come up any other time.)
Check the kernel log (dmesg) and /var/log/messages for clues.
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