I tried to add in a "change background" button to my site and decided to use the JQuery Cycle plugin. The cycle is working fine, but the background is no longer sitting behind all the content on my site - instead, it's sitting on top of everything. I haven't changed the order of the elements in my HTML file, and if I remove the JQuery statement that creates the cycle from the $init function, the background goes back to where it should. Any ideas?
The jQuery Cycle plugin manipulates the z-index of its slides. Most likely, a z-index higher than that of your other content is being assigned to one or more of the background images and, therefore, that slide (or slides) is displayed above the other content.
You can observe this by using a tool like Firebug or the native Developer tools in Chrome or Safari to inspect the images while they're being rotated by the Cycle plugin.