I tried the steps you mentioned but have had no success. I water the tree after finding it grown and then the hints tell me to take the pills from the desk but it doesn't let me.
Ah I'm guessing Isabelle is knocking on the door, you can skip that part by choosing the option "freeze in place" or something like that. Forgot about that part. The official in-depth walkthrough mentions that part too and explains how you can get past it without having to talk to her. So I'm assuming you mean that part.