I have created stairs up to a third level but all of the ground textures are invisible but work on the ones lower down. The walls seem to work fine though. Is there something that I am missing?

It is described in the Map editing page of the EFPSE manual.

Floor textures only work on the first floor and act as ceilings on the second and higher floors. Therefore, wall textures should be used as floors on floors higher than the second floor.