Cipro and good bacteria

I was given Cipro 500mg twice daily for a UTI. After 4 days on the medication I developed severe joint and tendon pain. Every joint in my body was in pain! I have called the doctor and they had me stop taking the medication. I continue to have pain in my joints. By the end of the day, my knees are killing me! Will this ever go away. I am seeing the doctor tomorrow, I am so upset over this, I am in my mid-30's and am feeling like I am 80! I am a grade 1 teacher and have 3 young kids at home, I hope things will get better!

Had My gall bladder removed in April 2007 and I was fine for months I had more back pain and went in for a cat scan and they said I have a Kidney stone and I was put on Cipro XL 1000MG for 7 days ever since now I have yellow liquid coming out of my backside all day and I have really Loose Diarrhea, Does anyone else have these symptoms from taking this??