It all depends. Do you have IBS right now, or do you have a prior history of IBS?
If you had a history of IBS and you haven't had it in over a year and are not on any medication to treat IBS, it may be waiverable.
If you have it and are on medication - I would consider the chances for a waiver to be slim - at least in The Navy.
I am not however, a Doctor. I also don't know anything about what Admissions does with waivers.
Since it's the service academy who initiates the waiver process and grants it or not, it's a wait-and-see thing for you I'm afraid.