Also - from the start, VRG got details written in to their contract (now in hindsight a VERY bad idea), and ensured DfT followed it to the letter. When the WCML works went overdue and downscoped, DfT picked up the bill for the Pendos. VRG paid no leasing fees for the 390s right until the end of 2009. So DfT is very bitter about that.
Also related to the WCML debacle, VRG threw toys out of the pram in 2001 and demanded a reprise to a 'management contract' as written into their franchise, ie they pay nothing but earn nothing. Even then they managed to make money out of the brand, extras etc. This went on till 2006 when normal service was resumed, with an agreement on the payment of the 390 lease.
Virgin XC also went on a management contract for a time during it franchise.
All in all, VRG has ****ed off DfT one too many times and cost it (and the taxpayer) a fair bit of money. Good commercially, good head about them, but it doesn't compute with what DfT want!