Sorry for all the troubles. It seems that you segment on oblique slices (you can see that from the warning icon displayed next to the segmentation node selector). This way when you paint on one slice, you actually paint on several slices of the segmentation. Unfortunately, fill between slices algorithm always works on the original slices, cannot work on oblique slices.
You can either try Grow from seeds effect (that does not require this strict slice-by-slice painting), or you can resample the segmentation geometry with rotated axes.
Knee MRI segmentation is hard, but it should be possible to establish a good segmentation workflow.
@carlp I saw some amazingly high quality knee segmentations from you. Could you help with some advice here? Or - it’s soon time for Christmas, so maybe I can ask such things - could you create a screencast video that shows how you segment a knee?