When I initially started this thread i was having this problem but found the fix halfway thru. Hopefully by writing this it can help anyone else in future need.
Client #1 (Problem client)
The UI scaling is automatically reset to 90% in windowed mode when clicking apply.
The option switches directly back to 90%…
Client #2 (working)
This popup window should pull up…
Click Yes… Worked…
Goto reset settings and scroll down under Reset Suppress Message setting to find Do you want to scale UI? Hit reset… Fixed
Resolution: There must be a bug if your setting have existed to block the ui scaling message that it would automatically reset to default upon apply button press. Resetting the message notification allowed the process to apply.