It would be best for you to work on getting used to both types of entries into the round off. You're problems with the run probably comes from the increased speed and not knowing what to do with it. My guess is that you're not leaning forward during your hurdle from a run, and are kinda pulling your shoulders back as you push into the hurdle which makes your hurdle go up instead of forward.
Try working up to the run two steps at a time. Do a two step run at the start of your next tumbling session, and to give your brain a head start, finish that session with 2 tumbling runs from a four step run. Add two more steps on the 2nd tumbling session, and you should be good to go.
I just want to add that some people like to start their runs by stepping forward onto the same foot they hurdle from. Those people need to start with a one step and work the same method. Most tumbling runs start with steps in the range of three to five steps, but a smaller gymnast may want to add a step or two beyond that to cover the distance needed to place themselves where they want to be in a floor routine.