Thanks for reporting and sharing a detailed description of this issue. I understand you have isolated the issue and a new slot works as expected.
Just to highlight, some configuration elements follow the content across a swap (not slot specific), whereas other configuration elements stay in the same slot after a swap (slot specific). -Example - Always On settings is Slot specific.
--App settings (can be configured to stick to a slot) - make it not sticky/clone and check.
With Deployment slots on App Service, they are live apps with their own hostnames. You have different versions of your web app to different URLs. You can test a certain version and then swap content and configuration between slots.
-- Based on your scenario - You may review the matching configuration/clone the settings as well/restart the WebApp and test.
Kindly see the doc section ‘Settings that aren't swapped’.
Note: With clone configuration from any existing slot. Settings that can be cloned include app settings, connection strings, language framework versions, web sockets, HTTP version, and platform bitness.
Kindly let us know how it goes, I’ll follow-up with you further and would need some more details about your WebApp and subscription (for which I’ll reach out you privately).