When you place tiles in the scene designer, Stencyl combines all of them in a single shape during compile. The same does not happen when you add tiles at run time. A better option is to use actors instead, and you could make one single big actor that spans the length of the 2nd floor, to prevent the snagging from happening. If snagging is the only issue, that should suffice.
Another option is to use one of the resource packs I made, which have behaviors for semi-solid platform support. In both cases, you shouldn't need to create the 2nd floor at runtime, instead you would place everything on the scene designer.