another possible cause of back pain is over recruitment of hipflexors, particularly illiopsoas, this muscle goups has proximal attachments on all lumbar vertabrae and has the action to flex the spine if the distal aspect is fixed, as in doin a cruch with feet anchored ect
Try doin your crunches with your feet raised and resting on a bench, this shortens psoas a little, and it becomes passive so takes the emphasise off them and allows rectus abdominus to work more. Also just concentrate on the first 30 degrees or so of the spinal flexion (the cruch) as research has found that beyond 30 degrees the hipflexors become largely active.
Also as mentioned above if TA is weak you will find it very diffiuclt todo any kind of situp as the spinal stability is not strong enough to provide a solid base for the movement to occur
I agree with this and most of the other replies as well. As far as I know research has basically "rubbished" sit ups and traditional crunches mostly due to the hip flexor involvement and constantly bending the lower back, which isn't really a good thing.
When I discovered this it made alot of sense as I experienced the same thing the OP described. Since then I only ever do reverse crunches, leg raises, hanging leg raises, and the 'kneeling rope crunch' - i'm not sure of the name but you can find it here
http://exrx.net/WeightExercises/RectusA ... runch.html
From personal experience, I noticed a big difference from doing these exercises.