It sounds like your FX loop is in series. You should turn off 'Killdry' on your Factor box. 'Killdry' is useful only when you have a parallel FX loop or when using it in an audio mixer with aux sends and returns. If you were to use a Factor box in an aux send & return on a mixer without engaging 'Killdry' you would experience phase problems with your un-effected (dry) signal.
