Chewy, were you letting the capsules dissolve -- or even worse, opening them up -- before swallowing them?? It's one med that you DON'T want to do that with, fer shure. A guy I knew in high school did that so he could smear it directly on his acne (hey, it made sense to him...), and it caused chemical burns on his skin.
Doxycycline is something that many people take long-term, as in years. Maybe you have an allergy to it?
BTW, it's a pretty general-purpose antibiotic. Very old-line drug, and there's quite a bit of resistance to it nowadays, especially since Bayer Pharmaceutical sells a shitload of it to farmers to dump into chicken feed.