As you can see from the klippy.logs, my firmware was configured to be minimal- display only for size reasons. Previously this worked fine on v0.11.0-218-gb389c70d for the display and v0.11.0-248-gd725dfd30 for the rpi.
Appears the problem is with the options for the atmega328p. Using this as the ~/klipper/.config and then make && make flash FLASH_DEVICE=... seems to fix it.
CONFIG_LOW_LEVEL_OPTIONS=y
CONFIG_MACH_AVR=y
# CONFIG_MACH_ATSAM is not set
# CONFIG_MACH_ATSAMD is not set
# CONFIG_MACH_LPC176X is not set
# CONFIG_MACH_STM32 is not set
# CONFIG_MACH_HC32F460 is not set
# CONFIG_MACH_RP2040 is not set
# CONFIG_MACH_PRU is not set
# CONFIG_MACH_AR100 is not set
# CONFIG_MACH_LINUX is not set
# CONFIG_MACH_SIMU is not set
CONFIG_AVR_SELECT=y
CONFIG_BOARD_DIRECTORY="avr"
# CONFIG_MACH_atmega2560 is not set
# CONFIG_MACH_atmega1280 is not set
# CONFIG_MACH_at90usb1286 is not set
# CONFIG_MACH_at90usb646 is not set
# CONFIG_MACH_atmega32u4 is not set
# CONFIG_MACH_atmega1284p is not set
# CONFIG_MACH_atmega644p is not set
CONFIG_MACH_atmega328p=y
# CONFIG_MACH_atmega328 is not set
# CONFIG_MACH_atmega168 is not set
CONFIG_MCU="atmega328p"
CONFIG_AVRDUDE_PROTOCOL="arduino"
CONFIG_AVR_FREQ_16000000=y
# CONFIG_AVR_FREQ_20000000 is not set
# CONFIG_AVR_FREQ_8000000 is not set
CONFIG_CLOCK_FREQ=16000000
CONFIG_AVR_CLKPR=-1
CONFIG_AVR_STACK_SIZE=256
CONFIG_AVR_WATCHDOG=y
CONFIG_SERIAL=y
CONFIG_SERIAL_BAUD_U2X=y
CONFIG_SERIAL_PORT=0
# CONFIG_SIMULAVR is not set
CONFIG_SERIAL_BAUD=250000
CONFIG_USB_VENDOR_ID=0x1d50
CONFIG_USB_DEVICE_ID=0x614e
CONFIG_USB_SERIAL_NUMBER="12345"
CONFIG_WANT_GPIO_BITBANGING=y
CONFIG_WANT_DISPLAYS=y
# CONFIG_WANT_SENSORS is not set
# CONFIG_WANT_LIS2DW is not set
# CONFIG_WANT_LDC1612 is not set
# CONFIG_WANT_HX71X is not set
# CONFIG_WANT_ADS1220 is not set
# CONFIG_WANT_SOFTWARE_I2C is not set
# CONFIG_WANT_SOFTWARE_SPI is not set
#
# Optional features (to reduce code size)
#
# end of Optional features (to reduce code size)
CONFIG_CANBUS_FREQUENCY=1000000
CONFIG_INITIAL_PINS=""
CONFIG_HAVE_GPIO=y
CONFIG_HAVE_GPIO_ADC=y
CONFIG_HAVE_GPIO_SPI=y
CONFIG_HAVE_GPIO_I2C=y
CONFIG_HAVE_GPIO_HARD_PWM=y
CONFIG_HAVE_STRICT_TIMING=y
CONFIG_HAVE_LIMITED_CODE_SIZE=y
CONFIG_INLINE_STEPPER_HACK=y