Field SW1 and SW2 using BOOT_SRAM boot loader?

I recently tried switching my firmware to take advantage of the custom boot loader’s extra space and in doing so discovered that the custom boot loader (make program-boot) appears to disable SW1 and SW2?

Firmware that reads these two switches without problems when not using the boot loader stop working when I switch. Are these switches being used for something else now? Is there any way to recover that functionality?

Thanks,
B