First ran into this problem after finishing nupraptor keep and being teleported back to the pillars.

Tried to use bat form to quick travel for the 1st time. The map comes up with all the beacons I've activated so far, I can switch to them but can't actually use them to quick travel no matter what keys I press. Tired it with default binds too and still no dice. Even the little esc button that appears on the map doesn't work, I have to press the actual esc key on my keyboard to exit the map.

Decided to just walk instead before arriving at the beacon on the snowy cliffs and realising that I need bat form to fly to malek's keep.

Try it again but its the same, I can select malek's keep but none of the buttons I press do anything. The only buttons that seem to work on the map screen are the ones for switching locations and esc for exiting the map. mouse right-click also exits the map, but left-click does nothing.

so I can't progress any further, unless there's something I'm missing.

Haven't quite figured out the correct sequence of what keys to press or where to click for fast-traveling either.
Surely someone more knowledgeable in the ins and outs can whip up an idiot-proof step-by-step guide?

Yep, that was what I was missing, thank you.

Strange, it work on CD version in normal way (enter or ctrl?).
Make sure game work not faster than 60 FPS. That can cause problems - as always can - with physics, controlling, GFX...

On KB i also change controls binding a little bit (again, on CD version). Gamepad always should be rebinded manually... for old DirectInput games and DInput input devices.
This game bundles with dinout wrapper, so this is not like old games. If you have Microsoft controller (or third-party xinput or xinput ones with dinput\xinput switchers) (also keep n mind wired and BT connections = differ devices, especially for Sony pads on Windows) - i guess it should (and better keep) controls as set by default. Not sure here.

Xinput devices should be more unific but instead they recognize as differ devices v1\v2\BT\wired\Ms ones\custom ones with xinput switcher\without switcher\Sony ones. Xinput-natively support games cannot predict all of this. Input wrappers can have own features-bugs.