If I make a change to a policy those changes are not getting applied to the end servers.

I have double checked that the correct policy is applied to the correct server under the configuration tab.

Any ideas

Is it that the policy is not applying, or that you cannot confirm if it has applied?

The Agent GUI (annoyingly) doesn't update according to the policy set - see here: 

How To Configure Group Policies (pulseway.com)

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We wasted a lot of time troubleshooting this, but this seems like a really basic capability.