I don't know anything about Pubit, but if your epub file displays correctly on your own Nook, I don't see any reason why Pubit should alter its look, if I'm reading what you say correctly.
One thing you might try - you can force the size of images in your epub file by using a style entry in the css file. For example, after I converted an rtf file to epub with Calibre, all images of a particular size had a class assigned by Calibre of .calibre5. The images appeared larger than I wanted. So I was able to modify the size of all of them in one shot by changing the style sheet using Sigil:
.calibre5 {
height: 32px;
width: 27px
}
If you didn't go this route and your <img> statements do not already use a class, you can add one to the css file and then type it into all your img statements:
<img ... class="myclass1">
and then modify the class statement itself in the css file to try different sizes for you images:
.myclass1 {
height: 700px;
width: 490px
}
Using this technique you can try different image sizes without actually modifying the images themselves, which is a big help in trying to get your epub to display correcvtly on the device.
Just an idea.