This was a problem before and you indicated the culprit was probably some of the plug-ins I've added to the site I am working on (camigas.org). I deleted a few that I weren't essential and haven't needed to make any changes until today. After adding a widget to the footer area, a good portion of my work in the theme options has disappeared. The video, donation links, and newsletter sign-up code have just *poof* disappeared. I have only 4 common plug-ins working on this site. I have used them elsewhere without problems.
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I had to fix the missing items quickly -- we simply must have our donation buttons (and everything else) up and running at all times.