You most likely have something corrupt at the main page type level for fields.  You may have to dig into the database to look for the structure and look for inconsistencies since it isn't blatently obvious within the Kentico UI.  The table definitions for page types are in the cms_class table.  You can look at the XML in the ClassFormDefinition field.  
Then go to the CMS_AlternativeForm table and compare the XML in the FormDefinition field and see how it compares to the base.  Order is defined in both tables by order of the nodes in the XML.