What Causes Severe Back Pain And Blood In Urine?

Hi, I am a 26 year old female. I am active, exercising 3 to 4 times a week and eat a healthy diet. I was hospitalized in July for 5 days with an infectious colitis I brought back from Mexico. I believe the bacteria was Clostridium Jejunum. I was on metronidazole and cipro in the hospital. I also had pylonephritis about 4 years ago in my right kidney for which I was also hospitalized for 5 days. Since my recent hospitalization in July of 2012 I have had right back/flank pain. The pain started when I was in the hospital and hasn t let up. It is progressively getting worse. I asked my doctor in the hospital how my kidney function was and she said rock solid so I was convinced it would go away. Finally, 3 months later I made an appointment because it wasn t getting any better. The cytology report came back as follows: Clinical Information and/or Impression: A) 40Ml Cloudy yellow fluid Specimen is received unfixed and labeled with the patient s name. ____________________________________________________________________________ DIAGNOSIS: A) Urine (ThinPrep preparation): Benign urothelial and squamous cells. No evidence of malignancy identified. They also did a creatine level which came back 0.9. I have no other levels so it is really hard to tell if it is trending up or not, but I think I remember asking in the hospital in July and it was 0.8 (not positive though). There was also trace amounts of blood in my urine. She sent me for a CT that came back normal for my kidneys and bladder. No stones or anything they could see. However, she did say there was an ovarian cyst on the right side 3.9cm by 2.5cm. She wants to watch this and does not seem concerned about my kidney. Could this be causing my back pain and the blood/cells in my urine? Should I see a urologist for my flank pain or continue taking IBU to help the pain?