Analog VGA has 15 pins, but 5 are grounds, so the 13 pins on that header would theoretically be sufficient. According to your first post, 3 of the pins are sitting at ground potential, which would be consistent with them dropping 2 of the redundant grounds. Furthermore, one of the pins on an analog VGA connector is supposed to be connected to the +5V rail, and you've got one pin that is sitting at +5V.
I'd say we have some good (but not conclusive) evidence that points to it being an analog VGA connector.
Edit: Just out of curiosity, is the header physically near the DVI-I connector? That would be the logical place for it if it is an analog VGA header, since the DVI-I port also has VGA-compatible analog signals on it.
Nostalgia isn't what it used to be.