As stated above - check your key fields and make sure your not duplicating data.
I would also think that the duplicate output error has to do with the field names you are appending to.
EG: You have two tables, TableA and TableB, both have an ID field. If you say 'Insert into ID' (not proper SQL i know), it is getting confused as to which ID field you have selected, or you have an output field named 'ID: NZ(ID,0)' which could also confuse it.
Also you will probably want two queries, one to insert new records (your append query), and another to update existing records (an update query suprisingly enough).