Although you say "I don't think she's referring to the choice between the left door and the right door", I think the context pretty clearly suggests she is talking about exactly that. In this scene, the Oracle and Neo are talking about his prophetic dreams in which he walks through "the door made of light" (which is later revealed to lead to the Architect's room), and then sees "something bad" happen to Trinity, and that "she starts to fall", but then he wakes up before he finds out what happens. The Oracle then says the reason he never sees what happens in these prophetic dreams is that "We can never see past the choices we don't understand", presumably referring to the choice the Architect gives him about saving Trinity or saving the Matrix from the danger of total destruction.
I suspect you may be taking her line "You've already made the choice, now you have to understand it" too literally, and thinking that rules out the choice about the doors since at that point in time he hasn't made such a choice yet. But I interpret this line to reflect her sort of timeless perspective on reality (compare with the real-life philosophical view known as eternalism), and that from this perspective all choices past, present, and future have "already" been made, and the moment of choice is just the moment we "understand" why we are going to make the choice that was "already" a fixed part of this timeless 4-dimensional reality. I think this interpretation is supported by the fact that immediately before the "You've already made the choice" line, she tells Neo "You have the sight now, Neo. You are looking at the world without time."
So, if we assume that the Oracle was indeed talking about the choice of which door to go through, he could only really "understand" the choice once he learned the full truth about the Matrix and the One's assigned role from the Architect (which apparently he didn't see in his prophetic dream), and realized his choice was between saving Trinity or saving everyone in the Matrix from near-certain death.
Here are the relevant lines, from part 4 of the Reloaded transcript here:
Neo: The machine mainframe?
The Oracle: Yes. Where you must go. Where the path of The One ends. You've seen it, in your dreams, haven't you? The door made of light?
Neo: [nods]
The Oracle: What happens when you go through the door?
Neo: I see Trinity, and something happens, something bad. She starts to fall, and then I wake up.
The Oracle: Do you see her die?
Neo: No.
The Oracle: You have the sight now, Neo. You are looking at the world without time.
Neo: Then why can't I see what happens to her?
The Oracle: We can never see past the choices we don't understand.
Neo: Are you saying I have to choose whether Trinity lives or dies?
The Oracle: No. You've already made the choice, now you have to understand it.
