Thanks for the post Roxanne. I don't or haven't used those programs before, and I will look into them.
I assume EEKeeper is for the Extended Editions, so I assume I will need to use Near Infinity.
I am going to have a play around a bit more to see if I can get anything to trigger by travelling around on the map a bit, etc. If I have to use NearInfinity, I am guessing I'll have to transfer the install folder over from the Pi to my laptop, use the tool, and then transfer the whole thing back, which is problematic due to the length of time it takes, but certainly possible.
If I have no luck, I may just complete everything that I can, and then move on to BG2.
The main thing that puzzles me is the fact that I can go to the upstairs section of the Flaming Fist HQ due to the stairs not working. At any other point in the game, trying to go somewhere may result in a combat situation, but certainly not in an inactive staircase. Very poor.