I agree with your assessments though I'm still not quite sure what's going on here.
I tried running the SPI line at SPI_SIXTEENTH_SPEED (32 divider) which is the slowest I could configure it to operate at and I'm getting the same results (SD errorCode: 0X2,0XDF). Again this only happens with 32GB cards (I haven't tried larger, though I have pretty extensively tried cards smaller than 32GB, at least 4 different types and they all worked flawlessly). The signals show clean on the oscilliscope though I will check this again to verify.
We do have pull-ups and caps on the signal lines.
The P1 module is running V0.4.9 (though I did try it also with V0.4.7), system threads are enabled (I did try it with them disabled as well though).
To recap the exact card I'm using is a Samsung 32GB EVO UHS-I Class 10 micro-SD card--my understanding is it should be fully compatible with other micro-SD cards. I'm able to successfully access (read and write reliably) the SD card using a different micro-SD board (non-particle though, so not this library and not this architecture) so the card itself doesn't seem to be the problem.
@ScruffR Unfortunately I can't easily try another chip select as the board has already been fabricated--this could be switched when the board goes to production if it really is the chip select pin though.
I guess my next step will be to try this code again on a standard Photon board with the off-the-shelf SD shield at a lower SPI bit-rate (have tried this in the past but am willing to give it another go) unless anyone has any other ideas?