Hi @terren,
No problem.
You are looking at 3 different distance matrices, which have different biological interpretations. Chris gave you links to the definition of those matrices in another post.
And I already provided you with a link that explains what the boxplots mean exactly. Finally, we discussed that according to your q-values, your groups are NOT different from each other. So I’m not really sure which part you are referring to when you say you are still confused, can you be more specific please.