burning, strange smelling urine, what could this mean?

You could have caught some sort of ual disaese. You said you "used a condom most times, only twice without", condoms prevent the spreading of ual diaseases so you could have very likely caught something from your boyfriend in one of those two times you didn't use a condom. The pill only kills the sperm, aka stops you from getting preganent. You should go to a doctor and get checked out, you and your boyfriend.