I had the same problem and I think I figured out some more details..

There were 2 systems that had been colonized by another faction that I took over by force, before my vines ever reached there. I then tried to add vines, but it kept deactivating after each turn. 

Then, once I fully eliminated the faction that originally controlled those systems from the game, the vine beacon worked on those systems. 

In my case, it has something to do with the fact that those systems were previously owned by another faction and that I colonized them before vines were ever present.

V 1.0.5 S5 Gold Public.