IPAK destroying Adv Firewall connections

Last month we have deployed the IPAK on windows server 2008 R2 servers, which later on found some Application has been stopped running. Found there was a firewall Inbound connections were in blocked state for all the profiles.

just wanted to know, when the MSN / IPAK deployments occur, will there be an changes occurs in the Adv firewall in bound connections.

Thanks

Arvin