You are going to have to give a whole lot more information before anyone can help. It sounds like you are using an emitter, and I guess some codes are working through the emitter which means it is most likely placed in the right area. It still may be a little off where all codes are not getting through. Also, the MRF350 has variable emitter outputs, have you tried adjusting the gain? There is also a IR port on the back of the receiver that you can use with the cable provided with the MRF350 (typically used for the antenna, simply use the cable with one end with exposed wires and screw them on to the terminals, leaving the other wire to plug into the receiver).

Let us know what codes are working, what codes are not working, if you adjusted the emitter ports and any other info you can provide.