Hi Daniel,
There was the issue of toolbar button checked hover brushes not being different from checked brushes that you reported yesterday but we fixed for the next maintenance release.
However I'm not seeing the other issues mentioned when I comment out all the theme code in our sample project's App.xaml.cs OnStartup code. Note that with all that commented out, some portions of the sample UI will look a little different here and there since ThemeManager.AreNativeThemesEnabled is not set to true by default. But everything else seems to be ok.
If you still think there is a problem, please make a new simple sample project that shows it happening and send that to our support address so we can debug with it. Be sure to exclude the bin/obj folders from the .zip you send so it doesn't get spam blocked. Thanks!