For sanity's sake you should keep the images in the Image(s) folder - it will drive you nuts later having them spread out all over the place. The only things I keep in the root are pages, css sheets, and scripts.
You are on a linux/unix box, make sure all your images & file names do not contain spaces (they will appear as %20) remove them, you can use underscores _ instead of spaces...also stick to lowercase in file names.
You can just delete the images from within FP and re-import them into FP and put them into your Image folder then replace them into your design.
Then Tools | Recalculate Hyperlinks
Then re-publish and see if that helps.
This is just for your images..but it may help the navs too.