I found the reason why the Adobe Flash Player Active X Control wasn't installing properly was due to McAfee Virus Scan Enterprise.
The Access Protection - Anti-Spyware Standard Protection module was causing the executables (when installing) to NOT accessing specific parts of the registry to complete the installation.
I've had to make the following changes to my McAfee policies in order to allow the Adobe Flash Player Active X Control to install successfully.
Anti-Spyware Standard Protection - Protect Internet Explorer favorites and settings
Processess to exclude:-
You might be able to make similar changes to your environment if you're using another product.
I hope this helps anyone who is experiencing the same issue that I was experiencing whilst trying to understand what was happening in our environment.
All the best,