Annoying glitch that won't let me finish the "Discerning the Transmundane" quest
From the UESP article about that quest:
To continue past this point, you must be level 15 or higher. If you aren't level 15 yet, giving Septimus the Lexicon will result in him dismissing you; then, you must wait until a courier delivers a letter from him to continue.
I don't know why the letter hasn't triggered, but you could use the console command setstage DA04 40 to force yourself to the next stage of the quest.
Alternatively you could try leaving and returning to towns to trigger a courier.