They had me on Cipro for over a year for a systemic staff infection that just wouldn't quit...I had never had tendon problems before, was extremely active (don't drive so walk everywhere) and suddenly I couldn't make it up the hill to the subway or over to the market...blew out my achiles tendons twice and it took years for my ankles, elbows and shoulders to come back...no one told me that it was the cipro or even warned me (to give them credit, they were too worried about the infection to care about my tendons)...now, over 10 yrs later I still have fragile achiles tendons but the others are much better...you can ask them to change antibiotics and see if that helps...you need to keep your limbs limber and moving but not over stressed...drink tons of fluids etc...and wait it out...You may need some sort of phisio if you are still aching after you stop it...walking in the pool can help a lot if you can get to one and a sauna or heating pad can is good for the general aches...but you need cold on the tendons if they are starting to hurt.
Sharon