Can't apply dot after creating note in note entry mode

Unless I'm missing something, this is normal and to be expected. Dots are part of duration. Like all other duration commands in note entry mode, they only affect the next note to be added, not any notes already added. See Note entry on the Handbook. Pressing dot after entering a note isnt supposed to change existing notes any more than pressing any other duration key does. Feel free to reopen if I am misunderstanding what you are saying.