I've written about this a couple times in the past. Hanging around with a serious Revit guru tonight I was surprised that he wasn't aware of the issue. He'd encountered it but had not sorted out the cause. The previous posts are THIS ONE and THIS OTHER ONE.
The essence of the problem is how the sketch is created in a workset enabled project. If you create individual segments so the stringers are formed properly Revit complains about having "two boundaries".
If you sketch segments that will not generate stringers correctly the stair will finish but generate another error. If you immediately edit the sketch and use the Split tool to break up the segment it then works properly.
Do the same thing in a stand alone project file and no problem. This is ages old but for some reason it only showed up on the radar when I submitted the issue back in 2007. Still with us today, go figure! Hey for those of you out there that I tried to blame it as "user error", sorry bout that! :) An apology is better late than never...