Returned it to the body shop, the service rep I'd been dealing with experienced the same symptoms I did. After about 5 minutes of pressing both FOB's, the trunk started opening consistently. He couldn't explain it. So I took it to the BMW service shop to have them take a look. After about an hour of checking out the car, they came back and said nothing was wrong (but they did change the batteries in both FOBs - even though the FOB's were strong enough to consistently lock/unlock the car and engage the panic alarm before the battery change).
Anyway, am glad it's working - but this was one strange experience.