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I came here to say the same thing, then figured it out. You need to click "turn on" next to time.

hmm, now it's started happening again even with time on :(

time on is time you were not playing an just speeds up your progress.
it works fine after you press the button to set everything in in learning tab to 0 as for what ever reason game coded to where it has false postive of you going over your limit.
so clicking set all to 0 fixes it