I can't really say how rubber guard could be affecting your knees as I haven't been rolling for very long, but I can tell you that when my knees swell and hurt it's usually because my quads and hamstrings are too tight. Tight muscles can increase the strain on tendons in the knee. Uneven musculature can also cause strain with stronger muscles pulling leading to a strain. Ice and stretching has always been good to me. Knee strengthening exercises would probably also help to stabilize and prevent injury.