OK, that says to me that:
The batteries are capable of holding a charge (especially if they can turn the engine over on their own after being charged from the donor vehicle)
The FV439 alternators are producing an output, but
The FV439 isn't charging the batteries
For a definitive test, if you've got a voltmeter to hand check the battery voltage when the engine is running and the donor vehicle is disconnected. It should read 28.5V +/- 0.5V with the engine at 2000rpm or above, if it doesn't then you've got a wiring or control box problem of some sort.
Andy