Did you try right-clicking the folder, selecting properties and then repair? Generally when a folder shows more of less mail read that it actually displays, there is a problem with the index which a repair fixes.
Same problem here, TB 102.3.3 / Windows. I have some filters which mark messages read after having them moved into folders, in TB 9x, the new messages notification never triggered/showed this with a red dot, since I upgraded to 102, I have the same issue. I repaired the index of the target folders, no change.