For this problem, make sure you are setting your speed mod correctly. Your speed mod must end in 5 or 0 (1.0, 1.25, 1.875, etc.) and you have to click "Set Speed" for it to work.
Another issue may be your key setup. Some setups will register three or more taps at once. If you're using something like askl and you find yourself having issues with taps not registering on a proper speed mod, try using another setup. If you have StepMania, you can check if your keys work together by going into Options -> Test Input. Try hitting all 4 keys together and see if they show up at the same time.
Hope this helps you. If you need anything else, ask.
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