I am not 100% sure this is the cause of your issue, but this is too long for a comment.
This can occur if SQL Server components are installed similar to the following:
- Install SQL Server Database Engine
- Install a service pack
- Install Reporting Services
At this point, the installer will refuse to install a post-SP CU due to the RTM version of Reporting Services. Based on my investigation, a certain registry value gets reset to the RTM version when Reporting Services is installed, and this is what the installer is referring to.
The solution is to install the service pack again (SP3, in your case), which will update Reporting Services, and then you will be able to install the post-SP3 CU.
I would assume this would be the case for other components such as Analysis Services, but I have only run into this issue with Reporting Services.