Ok I have the dark themes all set. ANd in my testing all looks fine...
But in doing it I noticed something odd... remember how I was saying there was a caching problem and I turned off the caching. Well in the dark theme, the logo was not displaying for me so I looked at the source code and the logo file was being named 2019logo.png.pagespeed.webp. I would go in the style and change the style URL for the logo to the correct path and it would change it back and add the pagespeed.webp to the end. So I searched and our webserver software has Google Pagespeed built in. So I researched more and found out that Pagespeed has a cache... and looking at it... well it was corrupted. So a quick clearing of the cache and restarting the services and now the logo shows like its supposed to.
So our issues probably were due to the caching... but not do to the caching I turned off but to the pagespeed caching built in the webserver.
Lesson learned..