I do think increased symptoms is often part of the effect of LDN. The difference is that the symptoms should subside once your body has purged a good share of the bacteria that are causing the Crohn's symptoms.
LDN works opposite of most other meds in that it makes the immune response work more normal instead of suppressing it. A normal immune system would never have allowed these pathogens to survive to begin with. That is my theory on it anyway.
I had depression on and off since I was a teenager. I am now 48 years old but only recently beat depression. It was tied directly to my Crohn's, more specifically, it was tied to the low grade inflammation Crohn's causes.
Once your body is done tossing out bacteria, and gets to a more normal state, you may also notice a change in mood. Depression may have more than one cause, but chronic inflammation is one of them. Just knocking down the inflammtion can rid you of the depression. Right now though, your immune system is causing inflammation because it is part of the immune response. Once that response is largely done, things may change.
You may want to consider using some supplements that can help you along. I use Krill Oil, Turmeric, Ginger, vitamin D-3, Magnesium, and Pycnogenol for many reasons, but the anti inflammatory properties of most of these is the big reason.
The Turmeric, Ginger and Krill Oil in higher doses removed my depression before even using LDN. The LDN has taken over for much of the effect, allowing me to take lower amount of these supplements.
I have been on LDN for over two years, and while it is not a cure, I feel it is as close as you can come to one at this time.
Hang in there, it should get better over the long term.
Dan