I got it working after installation you have to reboot. Then launch ISE so it can finish configuration of PowerShell and then reboot again (may just need to restart the Altiris services).
Now the PS 3.0 function I was trying to use was "Invoke-WebRequest". I would get the following error after the steps above:
Invoke-WebRequest : The response content cannot be parsed because the Internet
Explorer engine is not available, or Internet Explorer's first-launch
configuration is not complete. Specify the UseBasicParsing parameter and try
again.
To fix this issue, I had to login to each site server with the Altiris service account and launch IE and go through the initial config. After those steps PS 3.0 behaved as expected.