Looks like the problem has been solved, this issue was due to an oversight in the level generator where I was looking for file IDs instead of names, so different areas would have the wrong IDs!
Update 0.1.5 Progress!
I have made a lot of progress this update, new elevator system allowing for the loading and savnig of different areas.
There seems to be some major issues with this such as room entities spawning in the complete wrong location, so I will be looking into it and fixing these bugs. There also needs to be some optimisation work, which I will look into also.