It's now almost certain that the firmware is the culprit here. Went back to 15.1X53-D30.5 and the problem went away - all LEDs green as expected. After I went back up to 15.1X53-D210.7 the old problem reappeared - the LEDs of fan trays 0,1 and 4 were blinking amber without any indication of fan problems on the CLI.
The images used were:
jinstall-qfx-5e-15.1X53-D30.5-domestic-signed.tgz
jinstall-host-qfx-5e-15.1X53-D210.7-secure-domestic-signed.tgz
Opening a ticket now as advised...