Thanks for supplying your plan. It helped a lot with troubleshooting this issue.
First thing I would do is reset your walls back to their default heights. It looks like you've been manually adjusting the heights of those walls and you shouldn't need to do that for this plan. You can do this by going to the Edit Menu->Reset to Defaults. In the window that comes up, check the checkbox for Wall Top Heights and click OK.
Second thing is you've got rooms that are at different heights. They're not off by much, but just enough to cause issues. To correct this, open the room I've highlighted below, go to the Structure Panel, and then click on wrench icon next to the Ceiling value. This will reset the plate height back to the default value.
Third thing is you have built a second floor in the plan and it looks like this structure doesn't need that. To correct this, go to the second floor in your plan then go to the Build Menu->Floor->Delete Current Floor. This will delete the second floor and will place you on the attic floor. Your end gable walls may be invisible at that point, so you'll want to select them, open then for specification, and uncheck the Invisible checkbox on the General panel.