Tones
We will need some more details here. For example, what frequencies and tones are you having problems with? If I recall correctly, some scanners can display the wrong tones on search mode and then if they are programmed in it will result in the effect that you are having. The other issue is, on very weak signals you do need a stronger signal on a channel that is being received with PL tone than carrier squelch. In fact, a digital PL signal requires an even stronger signal than the one with analog PL. I don't recall all the details right now, but that is what I remember.