Why does my toddler have penis pain if he doesn't have a UTI?

My 14 month old started having fever on Friday. We treated it and have been watching him closely. The fever even got up to 103 yesterday. I called the nurse again and when I was talking to her I realized that he has been grabbing at his penis and seemed in pain. He has been doing this on and off for a week now and it has gotten worse. I guess I thought it was diaper rash bothering him, but now think it must be a UTI. Well, she had us come in with him to the clinic this morning to check it out. He has no other signs other than the fever and the crotch grabbing. She took a urine sample using a catheter and everything came out clean. The catheter experience was horrible and I felt so bad putting him through that, although I am glad it isn't looking like a UTI. Ever since the appointment he seems really bothered in that area. I don't know if it is from the catheter or if what ever it is is getting worse. I feel very helpless and want to fix the problem, but don't know how. I changed the kind of diapers, just in case that was it. We are giving him Motrin for the pain. Giving him lots of fluids. And just trying to distract him. Has anyone else ever experienced something like this? -Amber