In reply to mick.h: It probably isn't what you want to hear, but you should take a couple of weeks off, rest, and hope it goes away. Ignoring exactly this sort of thing ended up costing me a year+ of climbing, and I haven't run since.
If you must carry on, i'd say go and see a physio. It's possible that you are feeling referred pain from somewhere completely different in your back, in which case a physio will find where and give you exercises. I found that swimming was a great way to stay in shape, and actually helped with the pain.
Sorry! Taking the time to recover now may seem like a ball ache, but it is worth it!
C-3P0 on 26 May 2012 - cpc1-runc3-0-0-cust441.1-3.cable.virginmedia.com
Take about a month off from running but keep the other exercises up that aren't bothering you. Start the running again slow and steady and if you still get the same pain see your GP.
There's such a range of things it could be from a simple muscle imbalance to skeletal/nerve damage. Sounds to me like it could be sacral with you being a runner but your GP will eliminate that when he/she starts moving your legs all over the place in surgery.
Just a little tip that may be of use is looking in the mirror sideways and look at your posture, in particular the curve in your lower back. Does your bum stick out with a good curve in the spine or does it curl under with what seems like no bum. If your arse sticks out you may have overdeveloped back muscles, tight hip flexors and weak abdominals. If you have no arse you may have over developed abdominals, tight hamstrings and underdeveloped lower back. I suspect you may be the 'no arse' type being a runner so you may need to stretch your hamstrings, strengthen glutes and work on your lower back strength with thoracic extensions.