And in the file "fuel/app/classess/database/query/builder/join.php", where class Database_Query_Builder_Join extends \Fuel\Core\Database_Query_Builder_Join, the is a :
If that is what the profiler reports, than those queries have actually run.
I expect the issue is related to ORM object caching, because you are not using WHERE clauses in the ORM query, you hacked a variable where in using the condition.
Since both queries select the same products and origins records, instead of hydrating the result, the objects are returned rom cache for performance reasons. You could try to include
->from_cache(false)->
into your ORM query, and see if that makes a difference.
If that doesn't work, you might want to ping Steve ("uru") on IRC, he knows a lot more of the ORM's inner workings that I do.