I have just found this post:
https://discourse.myriadrf.org/t/custom-lms7002m-board-debugging/1746/6
Which points out there is an error in the MCU programming instructions linked above and 1 in bit 0 indicates that the buffer is empty. So there appears to be no problem.
It would be great if that documentation could be updated as we know there have been at least two people caught out by that typo.