Thanks for writing yor query.
After reading your post, it seems that your girlfriend is having urinary tract infection
, which cannot be detected in CAT scan.
Other possibility of high red blood cells in urine along with lower abdominal pain
is that she is having her menstural periods.
You should get her urine sample reinvestigated for Routine/Microscopic and Culture/Senstivity.
Encourage her to drink lots of pure water. She should drink atleast 8- 10 glasses of water in a day.
Treatment can be planned according to the reports ofthe above mentioned investigations.
I hope this is helpful to you.