I also had the warning in system center that my system did not have anti-virus protection
after upgrading Avast endpoint protection.
I looked at Microsoft's knowledge base, and they claimed this was a known issue with Windows 7 and
Windows 2008 - not specifically with Avast, but in general.. you may want to go take a look at this:
https://support.microsoft.com/en-us/kb/2482947( System health report doesn't detect antivirus programs in Windows 7 )
There is a US hotfix - I'm not sure about other countries, but after reading the description and obtaining
the hotfix, I applied and rebooted and it resolved the problem without uninstalling and re-installing Avast...
in my case, my avast installation was the result of an update from within the program, and not a fresh
install.
Windows action center no longer reports that my system is not secured.