This is normal. If anything, your orange channel is slightly over-compensated, you can see that noise favors the first part of the low level. You can probably make VPP measurement closer by adjusting compensation a bit. But generally, it does not matter.
The voltages look strange. Does X1 in the UI mean 1x probe? If so, switch to 10x on both the probe and the scope. 1x mode is mostly useless and compensation adjustment will not do anything in that mode.