I believe I found the core issue: geany really doesn't like Makefiles that spawn daemons, e.g. contain a target that executes `program &` or similar.
Workaround: as soon as the called `program` returns, geany can `make` again. In my case it's `evince`, which exits immediately if there already is another instance running (which then reloads the PDF in question), so this is very easy for me.
However, I believe that Geany should be able to `make` again as soon as `make` returns, so I do consider this a bug.
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