If your video hardware provides a reference signal input you should attach a stable reference signal to this input and enable the feature (in the software provided by the vendor). This will allow just:out to run synchronized and therefore more accurate which is even more important when using the redundant playout feature.
Using the AJA downstream keyer means that the video card synchronizes to the incoming video and not to the reference signal. Therefore any reference signal attached to the "Ref In" will be ignored, so make sure that the incoming video signal is stable. In order to stabilize the signal in advance (i.e. before it is sent to the video card input) you must use a frame synchronizer. Suited frame synchronizers can be found here: http://www.aja.com/products/fs