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@Gordon
@fanoush thanks - everything from address 0 to 0x100000 (1MB) is the same, and the UICR from 0x10001000 to 0x10001210 is the same. I'm not sure if I should be checking anything else?
I believe the issue is it's just not entering the bootloader at all. The bootloader should always turn the LCD on, and even if for some reason the LCD wasn't responding the backlight should come on which should be pretty easy to see.
The bootloader should still be fine if the SPI flash isn't responding too - but even if it wasn't by that point it should have drawn some stuff onto the screen that we'd be able to see. It's really hard to know what's up.