Diatoms tend to come with poorly filtered water. Are you doing a water change every few weeks with rodi that isn't 0 tds? That will feed them the silica they need. So will new rocks and sand, and not removing dead diatoms before they can rot and feed the next batch.
3 months isn't that long at all, they'll prolly wear themselves out in another month or so if you're doing the rest of it right.