I would highly encourage you to check out the Health pages here as well as the posts
that are also on MSK forum.
http://www.medhelp.org/forums/show/256
Do you have any stones?
It is possible either way for the infection to have never totally gone away and is now a chronic infection. Standard tests and treatments are designed to show acute infection not low level chronic infection so are based on colony count etc. You might try googling, chronic kidney infection and see what you come up with etc.
IF all else fails and the side pain doesn't respond to antibiotics, you might consider
seeing a good Pelvic Pain PT. I lived with the pain you describe for many years, and the PT found scar tissue no one else did and broke it up manually! It sounds bad but wasn't at all and the pain is now gone.. except when I am passing some sand as stone etc. I
Hope your feeling better soon!
Shelly