Losing Theme Settings and Customizations

Any time I move a blog/site from my dev server to my production box, I lose some/many theme customizations. This happens 100% of the time – I must go in and manually re-add all the customization settings. Today, we switched to a different theme, switched back, and all of the theme-settings had to be re-entered.
How/where are these settings being saved, and/or what would cause these settings to be lost or not come over when moving (via CPanel backup/export) to a different box?
We are using a child-theme if that matters.