SD card initialisation problem with Atmega32u4
I am using the original chip select pin SS (CS_1) for the SD card, and PB4 (CS_2) as the chip select for a CAN controller.
I am fairly sure the SPI interface is working OK because the CAN controller initialises

SD cards don't like to share the SPI bus. The out-of-reset protocol is not SPI, and the chip select works as active high. Thus your CAN communication on the bus could be mis-interpreted as card commands and put the card in a funky state.
Workaround: On Power-Up initialize the SD card first - this turns on SPI mode and CS changes to active low operation.