First off it would be great to know the version of the product you are using, as Altiris Helpdesk is an EOL 6.x product, and Altiris Service Desk is a 7.x product based off of the Altiris Workflow Solution?
The AD Import has a limit as to how many objects it can import in one go, so perhaps thats the problem.
When you configure an import rule, you can select what data class columns you want to map to which AD attribute.
You need to be careful with this though, as I believe that the AD objects have to have data in the attributes that you target.
By default, you need at least display name and given name, or something along those lines. I cant quite remember, sorry.