I believe that is it Alex. I looked back at my script and sure enough, it was installing the 32bit plug-in no matter what the OS architecture was. I have all of our agent/plug-ins scripted for our remote location installations. This way, they dont have to leave their machines online for a period of time while they wait for all the agents/plug-ins to be installed through traditional methods.
Oddly enough, we would have never noticed this if it was not for Windows 8.1. I have a Windows 7 machine, sitting next to me, that has the 32bit plugin on a 64bit OS and the SMA is behaving normal. Yet, once we do this on a 8.1 machine, SMA crashes.
I used the following query, in a filter, to find all of our machines that have the plug-in installed incorrectly.
select id._ResourceGuid
from Inv_AeX_AC_Identification id
left join Inv_AeX_AC_Client_Agent ca
on ca._ResourceGuid = id._ResourceGuid
where [System Type] = 'Win64'
and [Agent Name] = 'Altiris Software Update Agent'
and [Install Path] = 'C:\Program Files (x86)\Altiris\Altiris Agent\Agents\PatchMgmtAgent'
I am now able to target all of our "improperly" installed Software Update agents with the Uninstall policy since many of them are over CEM. This should allow them to uninstall and receive the correct install policy after Resource Membership Updates run.
Again, Thank you Alex for your help.