*SPOILERS WARNING AGAIN*
Just to make sure..... You didn't go to the Flower shop more than once after you got the clue, right?
Also.... Not sure if it will affect the results or not, but when you went and cooked with Papyrus, I asked all questions and did you go against the love interest you choose? (In my case I helped Papyrus in the food fight)... Again, not sure if these are needed to be not killed by Doc. Rose...
Or you could restart the game, and see if that helps