Electronic – What does SWITCH pin do on a microSD connector

I'm pretty sure the datasheet warning is there to cover the case where a pin is tied directly to Vcc or Gnd, but then the firmware configures that pin as an output and tries to drive it to the opposite state (either because of a bug or a subsequent firmware change).

If you really want to play it safe, put a relatively low-value (say, 1K) resistor between the card socket contact and the GPIO pin. When the GPIO pin is used as an input, this resistor forms a voltage divider in conjunction with the internal pullup that still allows the pin to be read as "0". However, if the GPIO pin should inadvertently be configured as an output and driven high, it serves to limit the current flow to a few mA.

Posting this answer as an excerpt of the comments, since the issue seems to have been resolved.

The registers in the SD card can be more tolerant to voltage drops than actual memory access, so this could be a power issue, perhaps you can check with your scope that the voltage supply to the card stays within 2.7 to 3.6 V the whole time. – apalopohapa

@apalopohapa Success, Looking at the input voltage, it was fine up until the ACMD41 init, then dropped down to 2. My boss pointed out a diode on a different page of the schematic that should have been tied low. Now I am reading everything correctly, and can continue. I'm just frustrated because time and time again I've had to tell myself to check power when having problems, and I can't just assume it's not an issue because it works half the time. I appreciate all your guys' help. – farraman