There was a Bug like this, don't recall the version, but I'm pretty sure it was fixed. Make sure you have the latest patch. If that doesn't do it, post back and tell us what version yo have and the OS.
The weird thing is I exported maybe a week ago with no problems and this started happening out of nowhere.
The version of CS5 I have is 7.0.3 and I'm running on OS X 10.7.2
As Peter mentioned, a bug like this involving overridden master page elements was fixed, I believe in 7.0.3. Have you updated from 7.0.0 to 7.0.2 or 7.0.3 recently? What if you avoid overrides?
Try exporting to IDML and also trashing your preferences.
Can you reproduce it in another document?