Just saw this Q.....
According to rabbit expert (that many rabbit-savvy vets consult with) Dana Krempels, "If you are absolutely sure this is blood, and not just pigmented urine (rabbit pee can be orange, reddish, or even brown, depending on what they've been eating), then she needs to be seen by a good rabbit vet ASAP so she can be spayed.
Uterine bleeding (which is what this probably is, if it's blood) is a sign of hyperplasia (pre-cancer) or uterine adenocarcinoma (cancer), and the only way to cure it is to have her spayed as soon as possible, if the vet does all the appropriate tests and finds her a suitable candidate for surgery.
There is a remote chance the bleeding could be due to bladder stones or severe urinary tract infection, but if she is a female and not spayed, then it is far, far more likely that the problem is her uterus, and it needs to be removed pronto (along with the ovaries)."
Please take your bun to a different vet (one who really knows a lot about rabbts) and have her spayed, otherwise you will not have her for much longer.
Have a look here too:
http://www.bio.miami.edu/hare/spay.html
http://www.rabbit.org/faq/sections/spay-neuter .html#why
Sorry to be so blunt, but I hope you will at least consider this.