Where do you transition from state2 to something else?
Are you trying to count all the rising edges, ignoring the falling edges?
Can there be a rising edge when you are already in a rising state? Like that second diagram where you have the stairs: is it possible to have input like that? If it is, then are you trying to keep a count of how many levels "up" you are right now, or should each rise be counted as one no matter whether you started from the base level or not?
In your first diagram, those pulses appear to have duration, so it seems plausible that stateflow is processing information in which the level continues to be high. If so you have a choice: transition back to base state as soon as you detect a rising edge -- or do not transition back to base state until you see the falling edge.
