Probably shouldn't have drudged up this old thread.
What you are showing in the logs is normal activity... radvd checks in every 12 hours, like clockwork:
Sep 18 12:32:10 ubnt-gable radvd[16414]: exiting, 1 sigterm(s) received
Sep 18 12:32:10 ubnt-gable radvd[16415]: Exiting, privsep_read_loop had readn return 0 bytes
Sep 18 12:32:10 ubnt-gable radvd[16415]: Exiting, privsep_read_loop is complete.
Sep 19 00:32:10 ubnt-gable radvd[30136]: exiting, 1 sigterm(s) received
Sep 19 00:32:10 ubnt-gable radvd[30137]: Exiting, privsep_read_loop had readn return 0 bytes
Sep 19 00:32:10 ubnt-gable radvd[30137]: Exiting, privsep_read_loop is complete.
Sep 19 12:32:10 ubnt-gable radvd[11529]: exiting, 1 sigterm(s) received
Sep 19 12:32:10 ubnt-gable radvd[11530]: Exiting, privsep_read_loop had readn return 0 bytes
Sep 19 12:32:10 ubnt-gable radvd[11530]: Exiting, privsep_read_loop is complete.
The "experimental package" was for v1.8.x
The radvd.conf file overwriting is not a problem under v1.9.0 to my knowledge. I suggest you open a new thread and post the relevant ipv6 router-advert config for review.