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After spending too much time on this in the past days I now stumbled upon the solution by accident.
If the section is declared before the beginning of the frame the problem does not occur.

My workaround so far is to add a dummy slide in front of the "multiplied" slide.
However this is very unsatisfactory as I am now practically forced to start my slide empty.

I have reduced the problem now to a much more minimal working example:
\documentclass{beamer}
\usetheme{PaloAlto}
\begin ...

Edit: For short version see my second post.

I am trying to make a presentation that allows me to click from one point in the list to the next. After some searching I found exactly the effect that I was looking for, but after compiling it a few times the table of contents is acting strange. For each ...