By default you can't have Shift and Ctrl as a paired control input, it will look like this:
With only Shift bound for up and no way to decrease thrust.
Also, if you remove the key binds for lift once the throttle is set, you can't change it. (I'd call that a bug.)
To use Shift and Ctrl as pair, you have to rebind them in the main options menu, like this:
Note that they remain bound to Propellers and boosters, respectively, until you allocate new keys to those inputs. So if you don't want to use Page Up - Page Down, ever, then this is probably OK.
I think the devs will have to change this limitation around a bit. Maybe they'll change the default key-binds for new players too...(?)
I moved this thread (back) to Unstable Bugs and added "[1.0.1.3]" to the title.