Hi, I also have version 2361 of Webroot Spy Sweeper installed.
Seems to be working just fine for me. As far as I can gather Spy Sweeper only shields IE and I only use IE for the Microsoft Update site preferring Firefox and Opera for my regular browsing.
But then again I am also running AdAware Pro, SpyBot S&D, and Spyware Blaster, AVG AntiSpyware, AVG Antimalware, Avira Antivir, and Agnitum Outpost Firewall Pro. So I'm staying pretty much Adware/Malware free.
Suggest you check the Webroot Spy Sweeper Shields tab to make sure all of your IE shields are turned on. If I recall correctly when I updated to version 2361 some of the shields did not automatically reset themselves to on.
Also you might want to raise the issue with Webroot support, they're very good at providing quick and useful advice.
Good luck.
