I have also found, in the Problem List area of the progress note, that choosing a previous diagnosis from the drop-down list often inserts the diagnosis ABOVE the chosen name. So you have to choose the name below your choice to insert the diagnosis that you want. It doesn't happen every time, not even on the same patient.
This started (for me) with version 4. I suspect something goes wrong with way AC pulls data from the database sometimes. Right now, it's just an annoying bug.