Here's my deal: I've got severe rheumatoid arthritis and I'm only 23. I've had it since I was 18. The Paleo diet has helped tremendously by making flare-ups a thing of the past, however there is still lots of inflammation. I'm underweight and always looking for ways to get healthy fats in me.
When I eat coconut/coconut butter, I feel great. I feel energetic, satiated, in a good mood, mentally clear. The problem is, my joints flare up like crazy. I'm not really sure why. Especially since coconut (butter) is touted as a powerfully healthful food. Hack away? I'd like to participate in the glorious coconut rainbow of goodness.
Either Tamandua is right and you're reacting to a protein (so just eat the oil), or you're not taking in more omega 3's to compensate for the omega 6's in coconut. Different fats differently modulate the arachidonic acid cascade that is central to the underlying inflammatory process in autoimmune disorders. You basically want a high 3 to 6 ratio to keep the dominoes from falling the wrong way.
So you could try taking more fish oil to compensate. Another solution would be to substitute good animal fats in general for coconut fat. Grassfed beef, freerange chicken, eggs marked as good sources of omega 3, etc.
Another thing that really helped me with being underweight and joint painy was to go strict gluten and dairy free. Good luck!
Coconut oil has almost infinite benefits. To get my daily intake (about 3 tbsp. for adults), I either put mine in my tea or coffe, throw it in a salad dressing. I recently made a smoothie ice pops with coconut oil, mango and banana - its a super easy way to get your daily intake.