Hi,
this sounds like it is getting removed from the database.
Can you please check the table #__update_sites using phpyadmin and have a look if the column "extra_query" is empty when this happens?
If yes, then indeed something on your site is wiping it. And that would actually be wrong as this is not meant to be for caching and must stay permanent.
What you also could try is manually purging the cache in the joomla update manger and right after that click on find updates. Maybe, whatever it is, it will fix the extra_query parameter in updates sites, as well.
Regards,
Tihana