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Click the box highlighted in yellow to change the pitch mode on the deck. The pitch mode determines whether or not the key (aka pitch) of the track will change or stay locked when you adjust the tempo using the pitch fader.
Think of MT (master tempo) as a key lock (changing tempo/speed does not change pitch).
Speed mode acts like a normal turntable would if you were mixing actual records, that means any change to the speed of the track will effect the pitch.
Hybrid mode has a key lock within +/-16% then outside of that range it acts like speed mode.
The problem I think you are having is that your deck is set to MT mode, and then when you scratch the pitch is not changing (which is why it sounds weird and digital). When scratching you get a lot of variation on the pitch depending on whether you are slowing the platter down or speeding it up, ect.
Try enabling key lock in VDJ and I imagine you will run into the same issue. I recommend using hybrid mode because the pitch of the track stays locked in a pretty big range, but when you scratch it will allow for the slight changes in pitch.
I hope that all made sense.
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