In the term metaphysics of presence does presence refer to a physical presence or a presence of time?
As is typical for Derrida-related concepts, the short answer would be something like both yet neither.
"Metaphysics of presence" refers to the way in which our thought privileges what is present over that which is absent. "Presence" in this sense can be a physical presence, a temporal duration, a presence in thought, a presence in speech—any mode of being-present.
An example of what is meant by the "metaphysics of presence" can, perhaps, be deduced from a passage in Plato's Phaedrus (Derrida has written on this dialogue famously in his essay "Plato's Pharmacy" published in Disseminations). In the Phaedrus, we find the following exchange:
Socrates I cannot help feeling, Phaedrus, that writing is unfortunately like painting; for the creations of the painter have the attitude of life, and yet if you ask them a question they preserve a solemn silence. And the same may be said of speeches. You would imagine that they had intelligence, but if you want to know anything and put a question to one of them, the speaker always gives one unvarying answer. And when they have been once written down they are tumbled about anywhere among those who may or may not understand them, and know not to whom they should reply, to whom not: and, if they are maltreated or abused, they have no parent to protect them; and they cannot protect or defend themselves.
Phaedrus You mean the living word of knowledge which has a soul, and of which written word is properly no more than an image?
Socrates Yes, of course that is what I mean.
Here, Socrates is expressly thinking of the written word as an image of speech. I may write something down, but what I write down most properly belongs to a dialogical context which will be lost in its being written. Unlike in a dialogical context, my written words cannot be subjected to interrogation. Removed from this spoken context, the written word loses its life. Here, what is favoured is the face-to-face context which is taken to be the more authentic means of communication, because in face-to-face communication, the person who speaks is present to us: we may question that person to see for ourselves if what he or she has to say is truly wise.
It is presence in this sense that is meant by the "metaphysics of presence." What is at stake is not the way in which something is present to us, but that we take certain modes of presentation as being more authentic and truer than other modes of presentation. What the deconstruction of the metaphysics of presence (ugh... what a phrase...) tries to do (roughly) is to uncover these more or less automatic structures of privilege and bring this structure of privilege into question.