If Rhythm and Roots is discovered by Raid Negotiator it doesn’t have both effects combined, only three 8/8 Ancients are summoned after 4 turns.
Tried it out and it worked fine for me 
https://hsreplay.net/replay/bsjmDHkbym3eXcomwuPeWM#turn=10a
You’re sure you had room on your board for the 5/5s ? Your opponent didn’t play Reno, lone Ranger the turn before ?
I just had the same issue. Was still forced to choose one of the options and the other one did not take effect.