The OS is on the HD. What is strange is that you have web interface to the unit. Which indicates it booted from the HD but has problems. Do you have full access to the web interface menus? The cooling fan is temp controlled.
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Double flashes reflect disk activity System is running a performing a disk check operation
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Allow it to complete the operation. may have not been shut down properly.
If it is blinking rapidly contionus means panic. When this happens you loose access to the snap. Hardware Problem in most cases.