Search button overlapping to the project's title in Frameless output

Can you try with a new, uncustomised skin and see if you get the same problem? If it doesn't happen, that suggests a customisation you made is causing the issue and you'll need to go through your changes to figure out what is causing it.

Perhaps first try setting adjusting all the toggles in the new skin to match your customised skin (one by one so you can tell if one of them is the cause). Then if none of them cause the issue, check the customisations on the search box, then the header. Those would be the most likely places I would think.