If my understanding is correct, kind of what bluedevils meant was to edit your shutdown cron script to include writing a 'flag' file when it begins to shutdown. This will place a file wherever you like which can then be tested for existence by a script in rc3.d when the system comes back up. If the file exists, it is clear that the system shutdown was as a result of the normal cron job, rather than an unscheduled halt, and the same script could then kick off the backup.
The backup script would need to be amended to include provision to delete the flag file once it is finished. If the system goes down as a result of an unscheduled halt, the flag file wouldn't exist and the startup script should be such that in this event the backup would not be kicked off. Can you post your shutdown and backup scripts if you require further advice, please? Hope this helps.