CT scan found a 9cm kidney cyst?

I went into the ER over two weeks ago with pain right under my rib cage, low grade fever, and severe nausea.  ER performed a CT scan and and ER doc said he saw nothing but small cysts on my ovaries which may or may not be normal.  I visited my primary the day after and she pulled the CT scans from the hospital and said the ER doc failed to mention I have a 9cm cyst in my kidney.  She sent me for an ultrasound and the ultrasound came back with nothing.  Am I missing something because I have no more fever, still have pain in the same area, and doc said my urine was "cloudy" which means a trace of blood.  The thought of a 9cm cyst scares me but now the ultrasound didn't see it!  I don't know what could be wrong.  Also, I am 2 weeks late for my period and I'm not pregnant because I've taken a million tests all came back negative!  Any help, please?