Ok, the issue has been resolved by doing nothing at all.
The alerts stopped on August 24, 9:52am.
Here's the log for that.
Event,Computer Name,Source,Risk Name,Occurrences,File Path,Description,Actual Action,Requested Action,Secondary Action,Event Date,Event Insert Time,Domain,User Name,Server,Client Group,Source Computer Name,Source Computer IP,Event End Date,Timestamp,Deleted
Virus found,client_server,Auto-Protect scan,Trojan Horse,1,C:\WINDOWS\Temp\DST7580.tmp,"",Quarantined,Cleaned,Quarantined,08/24/2010 09:56:02,08/24/2010 10:01:08,Default,SYSTEM,antivirus_server,My Company\SERVER\Servers - 32 Bit,,0.0.0.0,08/24/2010 09:56:02,08/24/2010 10:01:08,0
Most likely case could be definition updates. I did submit quite a few samples to Symantec.
Holding off on the upgrade for a bit later.
Thanks for all the suggestions. Great community here.