Pepakura Designer supports some file formats, but it may not load some files properly due to the 3D software version's saving options. Try changing the saving options, or convert the 3D model into another file format with other software.
Pepakura Designer has great compatibility with Metasequoia and Metasequoia supports a lot of common file formats. Please try Metasequoia. (Metasequoia is a 3D CG software developed by tetraface Inc., and is not our software.)