Try without the flags.
./autogen.sh --enable-gekko
Yes, that totally worked. Thanks! I don't have my BM1384 yet - waiting on a delivery from Sidehack.
There is a gcc bug in the Raspian image you have.
https://www.raspberrypi.org/forums/viewtopic.php?f=28&t=139091You might want to start a new SD card to get a clean image as -ck pointed out and avoid potential issues later.