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Altiris recommends to use the .exe based installation if there's already an older version of the Agent installed on the machine. That's the only way to do an upgrade (from at least build 2.0.1366 to the current build 2.0.1403). The .msi based installation forces one to first uninstall the older version and then install the newer version.
If you only have the .msi file by the hand you can do the update using the following command line:
msiexec.exe /qb- /fvamus <PATH to Software_Virtualization_Agent.msi> PRODUCT_KEY=<nnnn-nnnn-nnnn-nnnn>
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