Oh my god, the exact same thing happens to me!!!! I've been baffled by it for ages and it's even gotten to the point where I'm afraid to use other people's toilets when I'm at their place because it's so weird. Last time, I cleaned the toilet and I came back 20 minutes later and the water was black!!!
I've been thinking if only we could get someone to do a swab on our toilet, they may figure out what's causing our disease - my rationale, all pathogenic bacteria care about is transmission, if it's something that transmits via aerosol then it causes coughing or vomiting, if it's the fecal route it causes diarrhea. We obviously have a pathogen in our bowel that transmits via the fecal route and so will be shed in large numbers this way; in much the same way people infected with C.diff have a "cloud" of C.diff around them (the pathogens way of trying to be transmitted) after using the bathroom. The current problem is they can't can't find the UC-causing pathogen in the bowel because there are so many trillions of bugs in there. But if we could get someone to test our toilet, there would be significantly less bacteria there and only the most pathogenic would survive, thereby narrowing down the search.