I've never had an issue with nausea from taking LDN. If taken at bedtime, and the stated opinions of some say that it does it's thing in an approx. 4 hour window, I doubt that the LDN would be interfering with digestion, causing nausea once it has done its thing, and since it is a neurolgic, I also 'think' (just the opinion/gut instinct of someone with absolutely no medical or scientific training) that it wouldn't/shouldn't/couldn't cause nausea. Is it possibly a small flare? If the LDN is properly compounded, fresh, all that good stuff... it should be doing its thing. Mine has seen me thru some extremely traumatic events... relationship breakup, lingering death of a parent, troubles my kids have experienced, very bad bouts of flu and colds... you name it, and it kept on ticking.
Unfortunately, kids... whether battling an incurable disease or not, tend to catch things left, right and centre. I was at a b/day party for a bunch of pre-schoolers last week. Guess what? 3 of them came down with croup. At least it wasn't Whooping Cough. But, I digress. Keep a daily food diary, if it persists, then its time for another fun filled trip to the doctor. Wish I had a ready made answer/solution for you, but I left it inside my Magicians coat, which mysteriously dissappeared.