Incorrect cutting with filleted shapes

Hi all,

I have been trying to perform a cut between shapes in arranged like the following using cadquery master.


The filleted cuboids are cut from the outer round shape to create 'ports'.

When the cuboids are not filleted, the desired effect is achieved:


However, adding fillets to the cuboid edges causes problems. Sometimes cuts are not performed:


and sometimes, additionally, outer shape becomes mishapen - it is no longer has a smooth outer surface.


Does anyone know what might be causing this issue?

Thank you very much!