In the first, the IRS concluded that the aircraft owner did not have to pay the commercial FET when it flew on its own aircraft. In the second, the aircraft owners were required to pay the tax. The difference between the two situations seems to boil down to scheduling. The owner that gave scheduling priority to the charter company ended up paying the commercial FET, rather than the lower fuel tax, on its own Part 91 flights. Among other things, this means that the charter operator is responsible for maintenance decisions and crew rest and duty information at all times, regardless of the fact that the aircraft might be operated under Part 91 for the owner much of the time.
Maintenance is the most likely area of conflict.
The FAA holds the charter company responsible for the maintenance of the aircraft, but there are many ways that charter companies deal with that responsibility. If the flight department wants the charter company to delegate much of that responsibility back to the flight department, this issue needs to be addressed carefully in the contract. Control of the flightcrews is another sensitive issue. Many corporations trust only their pilots and do not want the charter company's other pilots to fly the aircraft. This can be negotiated.