Well, I see that this discussion ended, unfinished, as soon as we suggested to post a Revit file, just a reduced version of the file, with just levels, views, and stairs, because of this reason:
"I won't be able to...(post the file)... my boss doesn't want our floor plans posted online."
For situations like this, I have created a Consulting Forum, where offices can post their projects or families, in their own private subforum. The address is in my signature if any office is interested in this different kind of assistance.
I had a similar problem a few minutes ago. Then I watched a tutorial video and figured out the issue:
The plan region will not effect the stairs unless the stairs are 100% within the region. You need to pull the region lines a few milimeters away from the stairs (into your walls a little), and then it works.