This might be because the ePO policy with the changed updater list may not have applied on the endpoints yet. The product guide explains this well. It can be downloaded along with the product package from the download site.
If you still see issues, please file an issue with Mcafee support and they will help you out.
When I need run a program without restrictions of App Control I run a Server Task for Scan and Add programs in a specific path or directory, after this I insert the SHA checksum value of main exe or dll of the application on Binary Tab.
Put it in oberservation mode and see what comes back.
I would follow neelima's and bzielin's advice. The Product Guide (http://kc.mcafee.com/resources/sites/MCAFEE/content/live/PRODUCT_DOCUMENTATION/2 4000/PD24209/en_US/mac_610_mcc_610_epo_pg_en-us.pdf) have detailed steps on how to enable Observation mode after you have verified policies are being properly applied. The 'Create Whitelist' and 'Run diagnostics' sections might be helpful here as well.
Like neelima said, If you are still having issues, open a support case and they should be able to help you.