I don't know why it happens, but I noticed the same behavior on my own website project (SceneSpot.org). I don't think we ever figured out what caused it, but it's apparently a minor cache issue. Our simple solution was to create an intermedite page. When you hit submit, it would load a page that would say "Storing Preferences", and then refresh the prefs page. It didn't seem to be a time issue. It was more like a page-load-count issue.
Again, I don't know exactly why it happened. My buddy figured it out though, I think. But we still have the intermediate page...so I'm really not sure. I think he added a "Pragma: no cache" to our headers in Apache...that might have something to do with it.
--Coplan