I was able to find one article that said that ephedra can cause prostate problems, particularly if the person has other medical conditions. If the urinary difficulties only started after adding the ephedra then it's likely it's causing a problem or irritation of some sort. This makes sense if the urinary difficulties are at night, after being exposed to the ephedra during the day, versus during the morning (ephedra clears out of the tissues and the inflammation subsides).
Cut out the ephedra and see if the problems go away. If they go away, then don't take the stuff ever again. If they don't go away, see a doctor.