Update from my Reply #14:
Removed several (5-6) entries relating to ctfmon.exe from the registry. My first shutdown after editing the registry was also slow, as that is/was just removing the registry entries, so the process may have been running in the background. The shutdown at the end of the night was back to normal, but will still have to be tested over a few shutdowns, to ensure this is consistent.
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These types of action certainly aren't recommended, for many people editing the registry is the last thing that they want to do.