This does not happen when I am using WSJT-X 2.1.2, I do not even have to have the waterfall running and I am still decoding signals. The waterfall is just an operator visual aid and has no effect on the decoding of signals that I can see. My radio is Yaesu FTdx5000.
Louis,
you are incorrect, you could verify that by a simple test. The visibility of the Wide Graph window is not relevant here but the frequency span set on it is absolutely relevant. WSJT-X only looks for candidate signals to decode within the current frequency range of the Wide Graph display.