Make sure the it isn't busy trying to do an update. I have had this happen a few times, I have learned that it was in the process of updating and for whatever reason it disabled it. Make sure the DATS and version are up to date and give it time to complete.
If it appears to be updated and no other activity, then try running a full OnDemandScan if possible and also download MalwareBytes the free version and run a full scan using that. Clean all cache files as well (Internet temp, temp and Cookies).
Contact support if you continue to have problems
Moved to VirusScan from Community Help.
Can I ask why you specifically mention Protected Mode? The software uses IE and depends on it operating in default mode. If you want browser protection SiteAdvisor is there as is VirusScan scanning any downloads. Plus you can add extra protection such as WoT for instance.
What operating system and service pack is this please?
Protected mode is turned on by default in Internet, intranet, and Restricted sites zones but turning it one elsewhere may cause problems.
So do you mean IE Protected Mode or some other entity?