Here is my explanation as to what often happens when you start taking LDN and the strange responses you get in the way of symptom swings. It is probably not exactly right, but I think it is close enough.
You start LDN and all of a sudden your immune system is working close to normal. For the first time in years, it has to address all of the pathogens and other infections that have been doing nicely, living in your body.
This sudden turn of events is going to cause all kinds of strange and unexplained reactions. While Crohn's causes the big D because of the bodies weak attempts at sloughing pathogens, a normal immune response does exactly the same thing.
The difference is now, with the more normal immune response, there will be an end to it. Because your immune system is now working, the pathogens will be largely eliminated.
Until that happens, you will have D, but it should end in a reasonable amount of time. I do not know how long that is, but for a lifetime of accumulation it may take a few months.
Your testing indicates it is working as it should, so give your body some time to re-regulate itself. It has a big job to do, but it knows how to go about it, now that it has an immune system that is working.
Dan