>Both of the fields are set to text and 2 in length.

According to the query whenever a match is made on the item / part number and the count code is different on this match those rows should be returned in the result. If this is the case you might want to create two separate queries that include the code on a specific part number and compare them side to side to verify that no rows should be returned.

If you can confirm that the query is returning bad results (or if you already did) then I would try compacting/repairing the database just so you cover for any index/table gone bad.