I greet you, Vecko!
In determining the latitude by the Sun, two parameters need to be known: sun semidiameter and sun declination. In Silent Hunter 5, both of these parameters are different from the actual values. I took into account the actual for SH5 Sun declination values when compiling Sun almanac 1939-1945. It seems to me that nothing else should interfere with the precise determination of latitude from the Sun.
And I would also like to clarify, were you aware of the sextant techniques I talked about in my video "3 secrets of accurate celestial navigation in Silent Hunter 5" when you did your experiment with the Sun?