I'm actually having the same exact issue. Well, same execpt I only had trace protein in my urine once. But I've had 3 Urine Analysis within the past month and all are positive for blood. I've had both an ultrasound and yesterday had a CT Scan, both of which came back normal. I went to see a urologist on Monday and the next step is to have a Cystoscopy (which I really don't want to have!).
I'm sorry that you are going through something similar and I will try and keep you updated with any information that I gain.
Lupus, Secondary Raynaud's Phenomenon, Pernio (Chilblains)