Andy, Unfortunately I haven't downloaded your map yet, but some things to note.
- The stepon needs to be tall enough to encompass the entire model on the next floor up on the final stair.
- If the stairway is in an 'odd' start point, make sure you have an actorclip running under the stairway that acts like a 'false floor'. For some reason, I found this fixed a lot of my stairways that didn't have an identifiable floor in range, even if it was solid brushes they were walking up.
- There *is* a limit to how much a step can go up, however, it's doubtful you'd hit it without trying really hard to do it. Put a stepon brush across a wall, for example, and try to step on the roof. No love. One stair at waist height won't get you there, either.
- Is the stairway wide enough for the character?
Hope that helps a little. As to the rest, Matt can run circles around me so I'm not going to comment unless you can't fix it with his recommendation.