Customize Feature Not Working for Custom Theme
Permalinkbody {
/* customize_background */ background-color: #000000;
/* customize_background */
margin: 0;
width: 100%;
height: 100%;
}
#container1 {
/* customize_container1 */ background-color: #424242;
/* customize_container1 */
width: 85%;
margin-right: auto;
margin-left: auto;
height: 100%;
}
#container2 {
/* customize_container2 */ background-color: #0f0;
/* customize_container2 */
width: 760px;
margin-right: auto;
margin-left: auto;
}
#masthead {
/* customize_masthead */ background-color: #0f0;
/* customize_masthead */
width: 100%;
margin-right: auto;
margin-left: auto;
margin-bottom: 5px;
}
They show up under the themes customize button just fine but when I save it just defaults back to the original colors.
Has anyone else had issues?
I already tried clearing the cache....

If the former, then there may be another CSS file which is overriding your changes -- you can see the relevant files in the Firebug addon to Firefox.
If the latter (CSS file reverts), make sure that you have the proper permissions to edit the file. Typically, the file should have 755 permissions by default, but if you're not the owner, then 765 should probably work for you.