Using Spek to see if an audio file is really lossless after doing noise reduction.

What program are you using for noise reduction?

Goldwave (clipboard)

To answer my own question, I now see that Goldwave noise reduction has many parameters that I don’t completely understand. Each one ends up influencing the results on Spek, so I’ll have to try different settings of Scale, Overlap, FFT size, etc., to make things work.

That doesn't surprise me. I use an older version of Adobe Audition for LP transfers and other audio editing work (though I don't do much these days) and the level of complexity and number of settings in these programs can be staggering.