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Do you actively practice rhythm and strumming? I started scheduling rhythm practice 3 times a week (for 5 mins) a couple years ago and now have pretty decent rhythm. You aren’t going to improve at things you don’t practice.
Tony is VERY good about explaining the timing for the daily challenges, but because you are often focusing on several elements in the challenge the brain will tend to learn the one you are focusing on most intently which is most often the fretting hand. To get good at rhythm you need to isolate just the strumming hand. On the daily challenges try taking a few minutes of muting the strings with your fretting hand and just work on you strumming hand doing the timing that Tony has laid out.