First, have you been checked out by a doctor or chiropractor? I have a similar recurring issue, and it turns out I have a curve in my spine that creates an imbalance. For me, the "fix" has been flexibility more than strength -- since one set of muscles is always flexed and the other always stretched, seeing a chiropractor and doing yoga and stretches and the occasional sports-focused massage has made a huge difference, along with giving up the specific exercise that exacerbated it (e.g. running). For me, flexibility + lifting with proper form to build those muscles (deadlift, cleans) has been an almost magical fix. Except for this week when I overdid the rowing machine and set myself off again, grrr.
Other than that, I'd say see a chiropractor or physical therapist and get a list of specific exercises to target your particular issues -- they tend to be more boring (the cat/cow thing, superman, etc.), but if you stick with it, it helps.
And Pilates.