I agree with Steve (who has a very interesting post on mapping tables, by the way). The mapping load has some limitations the "normal" load does not. One of them is that it doesn't allow optimized loads and another one is that it doesn't allow either loading from multiple files using a wildcard, or joins, or so.
Bear in mind that tables are concatenated implicitly when they have the same number and name of fields. You may be loading the same table twice and the records will be appended to the first load. Is there any chance that this might be happening?