When I open multiple documents by marking them in a file explorer and hitting the enter key, Sumatra PDF overwrites the portable settings with a default version of the settings.
This also happens (unsurprisingly) when I execute SumatraPDF64.exe directly, instead of launching SumatraPDFPortable.exe.
I searched for registry entries pointing to \PortableApps\SumatraPDFPortable\App\SumatraPDF\SumatraPDF64.exe, but found none. All file associations point correctly to \PortableApps\SumatraPDFPortable\SumatraPDFPortable.exe.