Well I spoke too soon on 'fixing all the bugs' !
Starting to make some real puzzles/levels with the beam modifiers uncovered a lot of issues, especially when it came to activating things with the 'power' node to do things like open doors. There was an issue that the 'open' animation trigger would get called twice sometimes and end up with the door getting out of sync with the power being on/off. In the end I've redone the logic for all the beams from scratch. It took quite a bit of time to find out what was causing all the bugs and re-do them all but I think (shouldn't have said that!) I fixed them all now.
I also made a start on some environment art last night which I can start to make some levels with and figure out what they will look like. So far I have some simple walls, floor, windows and arches and a few miscellaneous props to decorate with, and once I get the overall room/s started I'll be able to see what works and what I need to set dress it. It'll be a fairly minimal environment, more about the overall mood and lighting than lots of details. I'm going to try to do it all without making textures too, so using single colour materials and geometry to make all the details. We'll see how that goes :)