When you upload to Pubit, do you then download a copy of the .epub file and look it over first? You can download it to your nook/nook for pc and check it out to see how it looks. I would also download a program called Sigil (http://code.google.com/p/sigil/) and use this program to help tweak your finished work before uploading again to Pubit.
Hope this helps!!
Did it look OK on the emulator. Maybe take it down immediately until you figure out what's wrong.
I agree with Melissa with both points--it is vitally important to check the entire thing on the emulator before you put it on sale, and Sigil has been a great help. I suggest you check it out.