Ok, it looks like I need more information to assist with this. What clustering solution are you using? In Windows clustering, patching the database instance should patch all of the cluster nodes but in the past, I've worked with Veritas clusters where I had to patch both nodes of the cluster manually. And to do that, I had to patch the first node, fail over, restore some key files and directories, and re-run the SP3 install on the second node.
When you run SELECT @@VERSION from each node, do you get a different result returned? I'm trying to make sure it's the database instance that's returning the unpatched release and not just SSMS. Are you using SSMS on your desktop or on the actual servers?