There isn't anything really wrong with the single row image. Your result shows a full 360 degree wide image. The image just needs to be centred, which can be done in a variety of ways. A simple way is to drag the image in the Panorama Editor window to the right with the mouse while holding down the shift key. The latter constrains the movement to be L/R with no U/D movement (like Photoshop). And on the Edit menu of the Panorama Editor, you will find an option to centre the image horizontally to get it exactly in the middle, like this:
I cannot say why the 3-row panorama has ended up with all the images apparently stacked together. PTGui can certainly stitch them. Did you just load in the images and run Align Images?
John