Neither a update config or even an agent restart sets the system back. It might be possible to run a script to reenable this setting, but I'm not sure of the exact values.
I found a similar script in regards to agent communication blockout. We would need to find the correct fields to populate for the bandwidth throttling. You could use it as a run script task in Task Server or DS.
Example (don't use this)
'vbscript
dim client
set client = wscript.createobject ( "Altiris.AeXNSClient" )
ignoreBlockouts = 1
client.UpdatePolicies ignoreBlockouts