I'm sorry that you are going through this. I have a somewhat similar situation with my husband, except, his inflammation started over 3 weeks after taking remicade, so we're not sure what's going on with my husband.
My husband had his last remicade infusion on Oct 6th, and around Oct 28/29 he started having pain in his left butt cheek. It got worse, and then he said his knee was hurting and his neck was stiff, and I noticed that his knee was slightly swollen. We figured the knee and neck was because he was compensating for the back/hip pain, and we thought he'd just pulled a back muscle somehow.
We went to an orthopedist, and he took an x-ray of the spine, and said he has inflammation in the Sacroileac (SI) joint,and suggested NSAIDs. We said since he has crohn's he isn't supposed to take nsaids, so we need to check with the GI. But by the next morning, his knee was the size of a soccer ball. So, his Gi ordered some blood tests (ANA and anti-histone antibody) to check for lupus, and told us to see a rheumatologist. In the meantime, my husband has had 140oz of fluid drained from his knee, and a cortisone shot in his knee, and is on 10 mgs of prednisone. We have also seen a rheumatologist and she is testing him for lots of stuff including Rheumatoid Arthritis, and autoimmune hepatitis, etc. For right now, his knee is only slightly swollen, but he still has a stiff neck and his back still hurts a bit . . .
I am hoping this is a reaction to remicade, and not anything more serious, but for my husband it didn't start directly after the infusion, it started over 3 weeks later! So hard to tell. And we're still waiting for test results.
But there is a test called the HACA that is done by prometheus labs, that can tell if your son has developed antibodies to remicade. I think when he is initally developing these antibodies, it may yield false negatives (because the antibodies bind to remicade to neutralize it, and therefore are not found), but once the acute phase is over, it should be measurable with the test. Please talk to your GI about this test. Also, please have your GI rule out other things, just to be sure.
Once we get the results of all the tests they've ordered, if nothing is really diagnostic we too will be asking for that test. I hope all goes well for your son.
Husband with Crohn's
Diagnosed March 2003 Ulcerative Proctitis
Diagnosed March 2008 Crohn's & C-diff, hospitalized 45 days
Canasa, Lialda, Remicade, VSL#3, Florastor
In Remission since June 2008
Stopped vancomycin for c-diff Jan 1 2009
C-diff free, until Sep 2, 2009
Fighting c-diff, I guess for life