It sounds to me like you're not taking enough medication to keep you out of a flare. You're on a dose that is lower than the recommended maintenence dose and it sounds like you're mildly flaring. Like Canadagal mentioned, most of us take around 3g of oral mesalamine a day and many of us use rectal meds as well. Your GI should really have you on a better treatment path. Have you gone in to see him since you've been having issues? that is another important factor in your case having records that you've HAD to see the doctor.
I still think going to HR is the right thing to do. I understand that the HR person is on the side of your employer but if they fire you for going to HR, you have a stronger case. Right now, it is wishy woshy. It is illegal for a company to fire you for going to HR to tell them about
the perceived mistreatment. If they fire you, it is considered retilation if they try to handle the problem, it is hard to have a case and the worst part is sitting around uncomfortable while you know they are talking about
you everyday hoping you breakdown and quit. You can't quit, no matter how uncomfortable or you have no case. It is hard to have a case now without taking the proper steps. You have to try to rectify the situation, that shows that you're interested in working things out and not just after a settlement. You won't get a lot out of a legal suit, maybe a few months salary. Maybe you could get disability but I don't think so because it doesn't sound like you're not capable of working. Even if you got a settlement for a few months pay, jobs are hard to come by right now so you end up spending the money living and if you don't find a job quickly, your family is in a bad position. Just my opinion and I am no authority on these things. I am not a lawyer or anything of hat sort. You should consult with some lawyers and see what they say. Best of luck.
I am in the US. Things may be slightly different in Canada.