Jethro,
EASA awarded EADS a civil supplemental type certificate for the A330 MRTT mid march this year.
Airbus Military awarded civil certification from European Authority
The STC covered the A330 modifications including the boom, enlarged cockpit with the Military Air Refuelling Console/Advanced Vision System, tanker flight control laws, and the universal aerial refuelling receptacle slipway.
The issue of the STC means the tanker works. What the aircraft is doing now is the military flight testing, which covers things which are not covered by civil regulations/procedures.