With S7 it is possible to designate the primary shuttlecraft at a spacedock. After doing so (and after still having a designated primary starship), the ship name displayed in space is the one of the shuttle. Only the displayed name is taken from the shuttle - the crew, hull and shields, weapons, abilities and bridge officers are those of the primary starship.
I have the same issue. Also, when I am setting up Duty Officer assignments and one of my crew gives recommendations, he/she says "I recommend the following candidates from the U.S.S. [...]" and it lists the name of my shuttle and not my ship.