I suffer from exactly the same problem on nearly 100% of recordings. Gain turned right down, recording from You Tube and other similar sources, clicks, moments of silence etc. Recording WAV at 4424 and 4824. Mac Pro 12-Core, Yosemite 10.10.5, Focusrite Saffire Pro 24 DSP (Mixcontrol 3.6). It all used to work fine until I bought the latest Soundtap. Careful not to do anything else while recording.
It is far too easy to overload the new Soundtap. Since Youtube generally does not have material above 0dBFS, Soundtap should be able to cope without winding back the gain to less than 50%. It would be sensible to provide a proper dB scale on the meters and an appropriate gain control (with a limiter?). Looking forward to some progress on tis, as it's being going on for a long time.