Electronic – SD card Sector size

Any moving of sectors that the device performs is translated automatically by the device itself; the data at any given address will read the same even if the device moves it every single time the device is accessed.

(Note that this is not true with MTD devices, which require you to handle... pretty much everything)

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