This sounds like an inflamed SI joint. I have chronic lower back pain that gets very bad when I ride or spin. I get one hip hitched up higher than the other, which makes my back crooked. Inflammation starts, muscles spasm and that's the end of that.

Stretching, especially your hip flexors, and icing it down are things you can do. Then get someone else to massage or do PT. I go to a chiropractor once or twice a month and he whacks my hips back in alignment and there's magic for a while with no pain. Then I do a hard ride or a rowdy spin class and it's back out again. I'm 5'1" and 57 years old and it's not going to get better, but you can learn to deal with it.

The worst thing you can do is ignore it... stretch, icing, PT along with ensuring you have the best bike fit as possible.. for a shorty, that is