I managed to get it working. I uninstalled amiberry, cleared the /opt/retropie/configs/amiga/amiberry folder. Reinstalled from sources, recopied various bios roms and ended up with this rom working:
kick40068.A1200 -> /opt/retropie/emulators/amiberry/kickstarts/Kickstart - 391773-01 (USA, Europe) (v3.1 Rev 40.068) (A1200).rom
I also ensured 755 permissions on the kickstart roms - they were 744 before. Not sure which of these steps actually fixed the issue though.