That is strange. It could well be an allergy, or as you suggest the pectin may have something to do with it too. No it won't be the sugar if you do ok eating cake!

What are you like eating tomatoes, cucumbers, etc? because some apples are very high in salicylate which is some kind of natural chemical present in certain fruits/vegetables and can cause a real reaction.

It's interesting that you mentioned this because I used to have something like that that occured when I ate an apple also and I think it was that chemical that did it. I also had amalgams at the time, so I wondered if mercury may have had something to do with Salicylate sensitivity or something or yes the pectin possibly increasing some kind of detox reactions.
It's strange I'll say that. Sometimes you don't know if it's a detox reaction or a genuine allergic reaction.

If it's organic, then it's certainly nothing that is ON the fruit. So whatever that apple contains, must set things off.

It could also be certain types of apples perhaps.