It turns out I have missed the fact that the VCCIO2 supply jumper is actually connected to the 3v3 rail on the internal power plane. This is caused by using normally open jumpers to create normally closed ones. The two pads of the jumper are on the same net and it is easy to miss the fact that both pads are connected to 3v3.
Fix this by using normally closed jumpers that only connect two nets within the footprint and keep the connectivity algorithm out of the equasion using a line on copper layer within the footprint.
It turns out I have missed the fact that the VCCIO2 supply jumper is actually connected to the 3v3 rail on the internal power plane. This is caused by using normally open jumpers to create normally closed ones. The two pads of the jumper are on the same net and it is easy to miss the fact that both pads are connected to 3v3.
Fix this by using normally closed jumpers that only connect two nets within the footprint and keep the connectivity algorithm out of the equasion using a line on copper layer within the footprint.
How to create such a footprint is described in the KiCAD forum: https://forum.kicad.info/t/creating-a-star-ground-component/3456/8
Close this issue when the problem is resolved.