What I was refering to was how you extract pending work from the DB2 database, not a configuration of BizTalk. The conventional way to do this is to call a procedure that returns one or more jobs to your bts app. It sounds like you are allowing both servers to see 'pending' work at the same time. By creating a unique identifier for each call you can trap the queue content so a subsequent call only reads new elements.
Something like trapguid =: newguid(); update pendingjobs set trapid = trapguid where trapid = null; select * from pendingjobs where trapid = trapguid;
There are examples of this in the bts samples sdk.