Chris, the pain does sound like prostatitis? Did anyone do a digital rectal exam, and was that tender?
Prostatitis often fails to generate cultures from urine or semen samples, because the infected area has got itself blocked off, but you really need a urologist who knows how to treat it rather than trying antibiotics.
Like Dave said, avoid stressing tendons while on Ciprofloxaxin. Many antibiotics are also mild anti-inflammatories and do generate relief while on them due to that, but then a quick return to former symptoms, which means they didn't kill the bacteria. So you'll have to wait and see how the Ciprofloxacin goes.
Do get hold of your PSA result. It's worth storing that away safely. Prostatitis often pushes PSA up.