The most like cause of this issue was that the restart compromised the AM6Taskfile.atl, which is found in the folder path below on Server 2003.
C:\Documents and Settings\All Users\Application Data\Network Automation\AutoMate 6
This file stores the task setting and trigger information, as well as which tasks are registered and the folder layout in the Task Administrator. If this file is damaged, tasks may not appear or settings and trigger information may be lost. The tasks themselves are stored separately and contain the step information for that particular task.
To avoid this issue, you can create an Automate backup job, using the AutoMate Backup AutoMate action. This will allow you to schedule a backup, which you can restore should this issue occur again.