The beacon effects last for 8 seconds, than they stop for a short time, and than they come back on.
Comments 4
I had the problem on a superflat world (singleplayer) with a couple of redstone builds (nothing too system intensive), but later this day I went on my server and there it worked fine.
Oops, found the problem, i once used the tiny structure filter and later forgot to remove all the commandblock-minecarts.
Are you experiencing lag in the system? I've seen this before with things like runaway villager breeders or mob spawners.