If it's not a kidney infection, my first thought is kidney stones (which is likely why the ultrasound). And yes, it's possible to have multiple issues at once! The antibiotics could easily have caused a yeastie, and yeasties don't always have a distinctive odor.

I'd call up your chosen clinic and ask if they can do more stuff than paps -- they almost certainly can, but it never hurts to check. (Unless the reception staff is incompetent, in which case you don't want to go there anyway!)

I hope you feel better soon!