I think I am having the same issue.
I have 2 CRS317 and 2 CRS328 connected in a ring. one of the 328 sees 1 interface as root port and one as alternate port - so everything works as expected but it throws those loop warnings in the log exactly once a minute.
also I have connected 2 ccr1009 to those switches via an active/backup bond. sfp+1 is its active slave and ether5 is its passive slave. I am getting exactly the same loop messages on this bond as well. as soon as i disable the passive(=inactive) interface ether5 the messages stop.
this is even stranger to me since as of my knowledge disabling/enabling the secondary interface should not be having any effect at all…
@ lleysan:
can you elaborate what exactly was your issue with neighbor discovery?
BR
Alex