As you can see in the screenshot, the 3 blobs on the left are identical to the blobs in the structure on the right.
When they are separate, slic3r manages to slice them correctly, as you can see in the bottom layer image on the left. On the right, however, when they are part of the structure, slic3r does not slice them correctly.
The difference between layer 2.50 and layer 2.60 is quite clear, as slic3r "jumps" to the correct slice shape.
Any idea what might cause this?
I have tried using the stl repair function, but the problem persists.