When you refill your Envelopes, the balances reset for the new month. That means that existing transactions won't appear in your Envelope bars. Instead, only when you add new transactions will your Envelope bars adjust.
Alas, no. I had entered some transactions for September before filling the envelopes, but I back dated the filling to Sept. 1. The transactions that I entered before the filling seem to be showing up, but, sadly, I did enter about 15 transactions before remembering that I hadn't refilled the envelopes. Is my only option to delete all of those and re-enter them? Please say no!