N-G Bonding Jumper problem
The bonding jumper should always occur at the first means of disconnect. Whether it is at the panel with a main breaker or a remote enclosed breaker. After that every panel or breaker should have an isolated neutral bus and a separate grounding bus. So you subpanel should be corrected.  

The meter is covered under NEC Article 90.2(B)(5) a. Which basically states that the NEC does not cover property owned or leased from the electric utility and includes you meter and meter base. So they have there own codes and we simply do what they have requested. 

Hope this helps.