It depends on if the flapper was made for that kind of toilet - some of the water-saving toilets use flappers that are designed to stay open longer or close quicker.
But - make sure the chain that connects the handle to the flapper is as short as it can be (while still allowing the flapper to seat.) i.e. - make sure there is no slack.
--Hope that helps. (Hard to say without seeing what's happening.)
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