Well I found other posts with similar problems and did a couple of them. I also found that the deployment agent was missing on my system so here's what I did:
1. Check if the package for the plug-in is correctly configured in the Software releases section. In my case it was missing so I imported the xml file from a good NS server but didn't work so I decided to remove it.
2. If the package is configured but is missing the actual msi file then delete it from the software library and run a repair for the agent through SIM. I ran the repair for the deployment agent 3 times until I finally got the correct files installed.
3. Double check again that you have the correct msi files installed and that you deleted the misconfigured packages from the software library.
4. On a command prompt run "aexconfig.exe /configureall" from "C:\Program Files\Altiris\Notification Server\Bin". Like many other people with this issue I had to run this command a couple of times, it fixed the software management agent on the first run but the deployment agent took a couple of times.
The aexconfig /configureall command takes about 20 to 40 mins to run and disables the console so plan accordingly when running it.