Thanks for reporting this. I've double checked the scene files and I can see the stairs issue but the ceiling is fine here. If you could send me the version you have I'd be interested to open it on my PC.
For the stairs, you're right. There's been a small change somewhere that means that the flat top/bottom values need to be adjusted slightly. For the treads a Flat Top value of 0.5m works well and the the balustrade a Flat Bottom value of 0.9m. I'm reluctant to change the files at this point because it would cause problems for users following the tutorial with older versions of RailClone.
I hope that helps, please let me know if you have any further questions.