D1, D#1 and Db1

So you claim the notes in the 1st measure to sound the same as the ones in the 2nd? Not to me, not at all

These notes are too low.
Perhaps they are outside the ability of your speaker/headphones to play, and you hear some of the upper harmonics (or artificial distortions).
Because they are very low, it can be heard a little muddy. But the difference between the notes can be distinguished.
It is clean with my headphones.

I don't have the problem either.
Maybe the reason is your sound-font. Which sound font do you use?

As I said before: These notes are heard as written. Below, you can see the frequency test:

Note: Maybe my tuner is not capable of capturing the last C0 frequency, but it can show C1 as the harmonics of C0. (Perhaps this frequency is more dominant; So this is a C note :) )