Well, are your pieces on the pepakura program overlapping the pages? If you are, that is most likely the reason. If not, check your printer preferences. If the layout of the pages on the program is in landscape form, and your printer is printing in protrait form, that can also be the reason.
I understand you are new here, and alot of such material are covered in the stickies we have provided. Check them out, gather what information you can. Also, doubling posting is not something the mods like to see, so try to keep it to a minimal. You can always edit your original post with your new information.
So yea, good luck to you, hope this helps.