Is your Master's program connected to a school that has a PhD in clinical psych already? That would improve your chances (as long as the school doesn't have a policy against taking students from their own Master's program). If not, you should hopefully have a lot more publications and research experience if your Master's program has been research intensive, which would help. Have you also practiced your interviewing skills? If you were rejected after the interview phase, that might be why. If you were rejected at the outset, perhaps it was your letters or the quality of research involvement, both of which will hopefully be rectified by your time in your Master's program. Ultimately, I think your Master's program has more of a chance of helping than hindering you. Good luck!