Vaginal Bleeding but gynecologist say it's not coming from vaginal area.?

I went to use the rest room and when I wiped, I saw blood on the tissue. Not a lot of blood. I am on birth control pills. It was loestrin 24. Now, I have switched to Ortho tri cyclin. I haven't been on them a month yet. I went to the gynecologist and she said I had blood and protein in my urine. She did a pap smear and looked under the microscope and said I had no infection. I had a pap smear 6 months ago and it was normal. She also did a urine culture and it came back with no infection also. She thought maybe it could have been a bladder infection. She determined that it was not related to my vaginal area and suggested I go to a urologist. I went to my primary doctor and they did a ultrasound of my kidneys and I haven't heard the results from it yet. It has been over 7 days so I'm assuming it's okay but I will call them tomorrow. About a week in a half ago, i did another urine sample and I had no blood and no protein in the urine. However, last night I used the rest room and I see blood again. Has this ever happened to anyone? What could be going on? I thought it was break through bleeding from my birth control pills but the gynecologist said it's not vaginal related. Also, I have had vaginal bleeding before and another gynecologist said it was from my cervix being inflammed. That happened in 2006. Now, I have seen blood on the tissue 3 times in about a month in a half. I assumed it was break through bleeding from my birth control pill but after the 2nd time this happened I said let me check it out. It scares me when I see blood. I would appreciate anyone who can help me out with this. Thanks for your help!