We got a really weird issue after upgraded to 6.3.5000. The issue is that the content (images and documents) in the dynamic module fields got switched. We actually upgraded from 5.4 to 6.3...following the upgrade path documented.
Basically we have a dynamic module with multiple fields to select uploaded documents. After the upgrade, the content(documents) in field1 now showing in field2.
This also happens to the image/media fields.