Hi CSNoc
I want to recap on the basics incase someone else does read this, but im sure you have done the first steps.
Make sure the policy you have changed, has been applied to the group that the machine resides in.
(Right click on the group, View group policy - ensure it correlates to the correct policy)
Ensure that the applicaiton control policy has ticks in the right places (Scanning tab in the policy, if you want it to scan with the on access scanner or the scheduled scanner - not having the ticks in the places you want, will give different results)
Ensure that in Sophos on the machine, the application control option has not been turned off. (You will see this with the alert:differs from policy)
After that, confirm if the communication is working correctly to and from the machine.
There is a file, 'View Network Communications report' on the machine under Start | Programs | Sophos
This will provide informaiton on if the communication is working correctly.
Further than that i would recommend you contact sophos to confirm the versions.
You can submit it online, instead of phoning if you want. 
