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.
https://gyazo.com/61b3a35edf8cd11ea69ba08e08526032
https://gyazo.com/5ce40f19ca115001a7b513ca605dddb6
The option switches directly back to 90%…
https://gyazo.com/61b3a35edf8cd11ea69ba08e08526032
Client #2 (working)
https://gyazo.com/61b3a35edf8cd11ea69ba08e08526032
https://gyazo.com/5ce40f19ca115001a7b513ca605dddb6
This popup window should pull up…
https://gyazo.com/04122b7e913f9ab5e021c8adcbcb4ce9
Click Yes… Worked…
https://gyazo.com/cb4d28f9ee268f0b4077a057d3cadf61
(FIX)
Goto reset settings and scroll down under Reset Suppress Message setting to find Do you want to scale UI? Hit reset… Fixed
https://gyazo.com/45963d03fcd19e39d649066ad1f6f1d1
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.