From various nutritional lectures we've known that coffee can be a cross reactor e.g. your body attacks coffee in the same way as gluten. So if you find coffee doesn't agree with you it's worth avoiding it for a while and assessing how you feel off of it.
Here's a video explaining more.. It's a controversial topic we know as there's limited published research on this in the UK although the USA seem to be delving into this further. This video should inspire some interesting debate: