If you are finding that the agent based reset guid command line isn't working for you, there was a resource pack/tool that was able to be imported in your 6.5 console that provided a task based approach to reset the agent guid if a duplicate was found reporting into the console.
I located the KB article here:
https://kb.altiris.com/article.asp?article=3848&p=1
The .xml files are attached in the KB artcile for import into your NS.
Definition
A Shared Altiris Agent Guid is a configuration problem that causes mismatched inventory data, and prevents accurate management and event-message storage of managed computers by the Altiris Notification Server. The Altiris Agent Guid is the primary mechanism by which the Altiris Notification Server uniquely identifies each resource record in the NS database. In this situation, we are concerned with computer resource records. There are several potential causes of shared guids. They all originate from circumvention of the normal agent deployment process, or external changes to the agent's configuration. The end result is that two or more managed computers each claim to be the sole owner of the Agent Guid (which is supposed to be globally unique).
Known causes
OS Imaging: By default, the Notification Server will generate a new Guid upon the first request from a brand new Altiris Agent. The Altiris Agent then stores its assigned Guid in the registry for Windows, and on the file-system for the Linux, Unix and Macintosh platforms. Shared Guids can be caused by imaging a workstation that already has an Altiris Agent installed. Each restored copy of the workstation will have the same assigned Guid. This issue exists in all imaging solutions, with the exception of Deployment Server (DS) version 6.5 or better. The best solution is to schedule the Altiris Agent to install immediately after restoring an image (This can be done as a DS job). An alternate solution is to always remember to delete the guid from the workstation prior to imaging (error prone).
Software Packaging: This cause is less likely to occur, but simple software repackaging tools will include the Altiris Agent's registry or file location of the guid as part of the software package. Activity by the Altiris Agent can fool the packaging tool into thinking that the Guid belongs to the package. Deploying the bad software package overwrites the good guid with the one from the capture station. To avoid this problem, don't install the Altiris Agent on the workstation used for snapshoting the original software installation job.
Resolution
The purpose of this document is to demonstrate how to use the Notification Server’s shared GUID diagnostics kit to successfully identify and remove computers within the Notification Server database. The attached MS Word document contains screenshots for additional clarity (it is now considered out-of-date, and is merely provided for historical reference).