There could be a caching issue. If so, it should go away within a few minutes - certainly within 24 hours (but almost always within 3-4 minutes). The folders containing those issues may cache when previewing (and thereby showing you old information in preview mode only) - depending on your browser settings or downstream ISP server cache settings. Ordinarily, clearing your cache or forcing a refresh will correct that. Published courses (publish preview, or publish live) will always reflect what the true settings are.
The ultimate test will be to publish (or 'extract') your course (from the 'distribute' button on the course). If it is still not showing what you are expecting, please let me know at knoesgaard@udutu.com and I'll look into it right away.
Also, some themes will let you set background images, and some won't. We need to better document which will and which won't. What is the base theme you are talking about, here? If you let me know which course/theme in your account you are struggling with, I can go in and take a look.