Did the person you were with perform oral sex on you?
I ask because there are lots of things that can cause infections in the urethra other than the normal STDs we all think of. If your partner had strep throat, for example, you can get the strep bacteria in your urethra.
Did they do a urethral swab or a culture on your urine to see what bacteria grew? If they haven't, that may be what they do next, a few weeks after you've finished the antibiotic.
Cipro is one of the first meds for a urinary tract infection, which blood and nitrites would indicate. It could also mean you have a kidney infection, too.
When you say things don't feel "normal", what does that mean? What kind of symptoms are you having?