The issue only happens on the upgrade path from the legacy product from SEE 8.2.x to SEE 11.0.1 and then upgrade to SEE 11.0.1 MP1, if your environment was built staring with SEE 11.0.1 then you will should not experience the issue.
Symantec has already had a SEE 11.0.1 MP1 HF1 which addressed the isse (intall and upgrade are different administrators). I have run a couple of tests in our environment and confirmed the issue was addressed.
With regarding your issue, since you have already had SEE management server succesfully installed, it is safe for you to uninstall SEE agent, encryption drive, removable storage and reinstall those components. One thing I noticed that some administrators does not check if there are any mmc process was running at the background, on server 2008, it started automatically, you will need to close the mmc process before running the SEE agent and other components upgrade, otherwise you will experience the error warning 25017. if you do not want to uninstall and reinstall the components, click OK when the erorr prompted to end the installation, then check the mmc proces and kill it (not just SEEM laucn mmc, some of the Windows console launches it as well), run the SEE agent and other components installation again, it will complete to the end.