I agree you need to look at your gait/ running style. Try mid-foot striking, then 'hinging-off' behind your big toe. Try shortening you stride so your lead foot lands just out in front of you and 'hinges off' underneath you. Make sure your hips are flexible and your hip flexors are not tight. Lack of hip extension will make you more inclined to heel strike and push off in front of you. Which will create more shock through shins and knees. Same goes for quads and hamstrings.
Because you're back in trainers are you heel striking more?? This will definealty push more impact force into your shins.
In my opinon orthotics are from the same school as plaster casts ('pots' up-north) and compulsory bed rest. Nowadays the medical profession minimise the use of both and i believe it should be the same with orthotics.
Feet are supposed to pronate - this is natures way of shock absorbtion. Stability trainers will change certain movements that your feet (and shins) had become used to in the Vibrams and caused the shin pain.
My guess is lack of driven internal rotation of tibia from the subtalar joint at foot strike (in stability trainers) has created a torsion effect because of top-down internal rotation from your femur. Your shins have flared up because of your history of 'shin-splints' and they are the weak-link in the chain. But i can argue that with a podiatrist!?!
I would get your ankle joint mobilised and your calf/ thigh / hip muscles stretched and deep tissue massaged. Tweak your running style and prob go back to Vibrams if thats what you're happier in!