I have a very similar problem. No matter which file (STL or OBJ) I try to open, Simplify3D will complain about "Cannot auto arrange. Largest part exceeds build dimensions". I removed the option to auto-arrange, and while it will not complain anymore, the objects will not be visible at all. From the "inspector" for objects the scale, size and/or position will be at a very high number (typically 9999,0% or 999999,00 mm), trying to change will not make any difference.
However when I try to import the file using the "Recent Model" menu, the objects import just fine (including using the "center and arrange" button).
To show that it is not related to the models I have used, I created an object using the "Add-In" for converting a bitmap to 3D-model. Exporting that as an STL and importing it into Simplify3D, will also be impossible – except using the "Recent Model".
I attack here both the factory (after "Import Model" and after "Recent Model"), including the STL-file.