Why are you using an oscilloscope for static voltage measurements? Use a multimeter instead. It's far more accurate.
I may be able to get a precise reading, but I would hope that a $20 Radio Shack multimeter is not more accurate than a $400 Rigol scope!
And I don't need a precise reading to tell that something is seriously wrong. But I do need more practice with my scope!
Is there anything else connected to SD_MISO which is not shown in the schematic?
Only the microcontroller and the ISP header. And nothing is attached to the header.
Are you sure the resistors are the values you think they are?
WTF? R4 is reading 129 ohms!
But I just checked five more of these boards and R4 is 10K as it should be. Which makes no sense as these boards were all assembled by machine. (The resistors are 0402 so there are no markings on them to tell me what values they are.) I suppose I might have gotten unlucky and picked the one board that had some rework done on it after that resistor fell off during reflow? (I don't actually know that any boards had rework done on them, I am merely speculating.)
I guess there is a slight chance I damaged the resistor while removing R6, but R6 and R4 are separated by R7 on the board. They're laid out side by side. So I don't think I could have damaged it with heat, and I cleaned the board up with alcohol and I don't see any damage to it, and it's measuring the same 129 ohms after I cleaned the flux off.
And I still don't understand what's going on. R7 is 470 but I removed R6, so there is no longer a path to ground. So why am I reading 2.5V when I probe a 129 ohm resistor connected to a 5V supply?
Using the voltage divider calculator, if I assumed there were a short across R6 so I had 470 ohms to ground, I should get 3.9V there. So that's not the culprit. Hell, I don't even need the voltage divider calculator to know that I would need another 129 ohm resistor to ground to get 5V down to 2.5V. But there isn't one! This is really weird.
Anyhow, I should probably run all my tests again on one of the boards with the correct 10K resistor on R4 and see what results I get. Perhaps my MicroSD cards will just start working again.