Came across this before, its something to do with the embedded voicemail system on a 3300. Theres a few things that cause this, most of the time you can temporarily get rid of the lights but at 3am the voicemail system either resets or performs some form of check which caused this to light back up. It may not work but a couple of things to check:
If this is embedded voicemail, go to the voicemail hunt group and make sure all voicemail ports are in the same hunt group, especially the first and last ports you have available.
If you are using RAD ports for anything and have a RAD hunt group, make sure the first and last voicemail port are not included in this group.
Other than that, has the voicemail system been restarted via the shell or the system rebooted?