This was seen on Apex 4.2.2 - maybe it has been fixed in later versions.
Note: The possible cause could be the use of the ApexLib APEX Developer Addon (version 0.95.21) - this was used while editing the applications (in Firefox) and might have something to do with the text field not being updated.

Scenario: You have 2 (exactly the same) copies of an application on 2 different servers, e.g. Dev and Test. You have an LOV with an SQL query in the application, and use it for 1 or more page items. You change the LOV definition in Dev, export it (using Component Export), and import it in Test.
Problem: On Test the page item still uses the old definition of the LOV.
Solution: Edit the page item (set "Named LOV" to "null", clear the "List of values definition" text field, and reset the "Named LOV" to the LOV you need. Apply Changes, export the page from Dev and import it in Test.
Note: Maybe this also applies to other import/export scenarios and/or Static LOV types - I didn't test that.
Note: The example (and query) given here only check page items. There may be other objects with the same problem; report columns seemed like a good bet but those don't seem to have this problem. Others may however.

Check query (for page items):
select * from ( select pi.page_id , pi.item_name , replace(pi.lov_definition, chr(13)||chr(10), chr(10)) as lov_definition , replace(a.list_of_values_query, chr(13)||chr(10), chr(10)) as list_of_values_query from apex_application_lovs a , apex_application_page_items pi where a.application_id = pi.application_id and a.application_id = 108 and a.lov_type = 'Dynamic' and a.list_of_values_name = pi.lov_named_lov ) where list_of_values_query <> lov_definition order by 1