I was highly prone to them as a child. It peaked when I was 8 and was sent to hospital to have scans on my Kidneys etc. I had to get a catheter (sp?) in. I remember it VIVIDLY! Thankfully my kidneys were fine and it was put down to frequent UTI's. I triggered them by not going to the toilet until I was bursting and sometimes going to bed needing the loo.
I very rarely felt 'ill' though. Does she seem in pain as she wee's?
It was very painful as Cystitis is now. Have you had cystitus yourself?? If so, you'll appreciate that it's uncomfortable, but doesn't make you sick or give you a fever. I think you would have to leave for a few days or more before it got that bad! I think your GP is being ridiculous. If he found any traces of blood or protein in her Urine then it's most likely to be a mild infection whether she is acting ill or not.
No advice to offer I'm afraid, as you seem to be doing the right things by taking her to the Doc and making sure she drinks lots. What about Cranberry juice, maybe you could try her with that.
Let us know what this 2nd sample shows... good luck.