It sounds like you are suggesting that perhaps the images are in the wrong folder or something and not showing up (or I am reading your post wrong).
What I am suggesting is to verify what you've done. Many people make changes but don't verify their work, so they don't know if something was done incorrectly and sometimes when they do, they don't know how to correct it. If your images are showing where they should be then that is not the problem.

Speaking of which, maybe I'm not understanding your specific problem? Having used IH2 I know that I can use the features/functions within Zen Cart to resize images as desired. There is or should not be, any permission problem as both the Admin upload and FTP upload will correctly use account Owner permissions. If you are perhaps using a 3rd party script for image resizing then that would be another story.