In a game with both the Fleet and Star Chart projects, Star Chart failed to offer a topdeck choice on the shuffle leading into the extra (Fleet) turn. Herbalist, also in the game, did offer a choice of treasures (which happens before the shuffle). See Game #20701355.
Interesting bug. I assume that something was coded to prevent Star Chart from bothering you in normal games when the game is over. But that needs to account the possibility of Fleet.
I just found this bug as well. Confirmed with the bot in game #26471319.
(It's a known bug under "Renaissance bugs" at http://forum.shuffleit.nl/index.php?topic=1226.msg3671#msg3671 (http://forum.shuffleit.nl/index.php?topic=1226.msg3671#msg3671).)