Because some stuff such as avionics is especially hardened for military use.
Though the bog valve in the VC-10 was a squash ball that BAe were charging the RAF something like £80 a pop for.
Didn't the Nimrod AEW 3 suffer a similar fate, as there was no fixed price on the contract, so a lot of money was spent trying to compress down the software for it onto the hard drive in the system, where the simple expediency of increasing the size of the drive would have cured it? but of course BAe wouldn't be getting paid then.