I never saw this thread before, but I know a lot about the cause of the issue, so I can contribute some information and things I've noticed.
This bug only affects the numbers in the right column for taiko, the Geki/Katu which is supposed to determine how many big notes you've hit, and doesn't affect gameplay at all. These numbers are completely broken. Gameplay is unaffected because the game will still give you credit for hitting a big note with both keys if the two keys are pressed within a small ms window. However this won't be counted as a Geki/Katu despite getting the full score (if a normal note gives 300 points and a finisher gives you 600, you would get 300 points twice).
You only get a Geki/Katu if your keypresses were on the same input frame. If you get 60fps, they will probably always be recorded correctly since you have a 16.67ms window. If you get 2000fps, then you have a window of 0.5ms, which means you'll very rarely have them recorded as being on the exact same frame.
An interesting thing is that this is also keyboard-dependent. Certain keyboards, mainly cheaper membrane ones, need to be sure of which keys you are pressing when you press multiple at the same time, because they don't have separate switches for each key. Because of their polling rates and how they have to check the signals, the output keypresses are usually sent at the exact same time, even if you pressed one key 1ms before the other. So if you use a membrane keyboard, you will usually have all finishers be recorded correctly. Mechanical keyboards with separate switches for each key don't have this problem, so players who use mechanical keyboards will rarely have finishers be recorded if they play at a high enough framerate.
I'm not sure how you could go about fixing the Geki/Katu numbers because in reality you aren't getting double score for the finishers, you're getting the normal amount of score twice. It adds up to the same score, but those numbers are completely meaningless for now.