1) Checking the framespec-file
The frame-spec file indicates the positions of the markers on your calibration cube. If you used Brown U. "Cube 1", the framespec file can be found here. If you built your own calibration object, you have to create your own framespec-file.
After you created your framespec-file, open a new maya scene. Use the import function on the XROMM shelf and import your framespec.csv file as 'xyz' data and beads ('bb') (uncheck 'rows are time series'). You should get a regular array of beads that resembles your calibration object. One plane should be aligned with the grid in the scene and one bead should sit exactly in the origin (unless you did not assign 0/0/0 to a bead).