So, I started off by looking at a few individual machines that were reporting as unhealthy and the client software on the machines seemed to be only partly installed. Due to this I looked at the client log files located here:

 c:\windows\ccmsetup\logs  

Within here I found some installation errors with the pre-req installations for the client. So I tried to run the MicrosoftPolicyPlatformSetup.msi file manually and it popped up a UAC (User Access Control) message wanting me to allow the program to run.

Out of pure curiosity I wanted to disable UAC and then push out the client from my ConfigMgr Console and see what happens....so, I manually disabled the UAC on three of the machines, rebooted them and then pushed out the client to re-install again, it then fully installed the client without any pre-req errors and then it reported back as being healthy after the ccmeval had run.

I then made the decision to disable the UAC on all machines using my ConfigMgr Group Policy (we have an environment where we do not need to have UAC enabled for any reason at all, yours may be different) and allowed this to be applied.

I've since got all but two of my clients running healthy!