It’s not entirely clear from the pics, but it looks like the nut termination is causing the problem. The nut should terminate the speaking portion of the string at its very edge with a “cliff.”
Your cello’s nut appears to have been trimmed improperly in an effort to lower the A string height. The nut seems to slope down as it ends, creating a curved and indeterminate contact point.
This is very much like a sitar bridge (jawari or Jivari), in which the termination is a carefully curved surface which interferes with the pulse train traveling along the string, causing the pulse to break up and shift the string’s energy to the higher partials. That’s what gives the sitar its characteristic nasal twang.
I once got a desperate call from a professional musician former student who stated the she was getting married the next morning and at the rehearsal, the piano sounded like a sitar! Sure enough, one of the strings was terminated with a ramp shape (poor bridge notching). A few swipes with a sharp knife cured it.
So, in your case, if the luthier judges that there’s enough ebony left to do so, I’d have the nut re-dressed to make it terminates cleanly at its edge. Or, possibly better, just have a new nut made.