The BBC is convinced that Brown is not a fan and, at the least, not as wedded to existing broadcasting structures as his predecessors.
The most alarming possibility is that Brown does not like the BBC, either because of what it stands for, or more probably because of past slights at the hands of BBC programme-makers. Courtesy of whole rafts of BBC analysis, we know that Prime Minister Brown has considerable talent for bearing grudges, and treats criticism by friends as tantamount to an act of betrayal.
It is difficult to even imagine how angered he must have been by the virtuoso performance of Newsnight the evening before he finally became Prime Minister.
The gonzo journalism by independent producer Jamie Campbell made riveting viewing. He simply followed Brown around for five weeks trying to get an interview, a comment, a wave of the hand... anything. The fact that he got nothing at all demonstrated just how controlled and controlling the Brown Project really is.
Given how strong the reality was in chronological order, it was unfortunate that somebody thought it would be a good idea to take two sequences shot two weeks apart, reverse the order and imply one caused the other.
There are other explanations for Brown's lack of warmth for the BBC. He could see it as greedy or believe it is trying to be aloof from the process of modernising public institutions.
As a senior figure in relations between the BBC and government muttered privately last week: 'There are a lot of fences to be mended.'
A couple that has drifted apart can sometimes be reunited, but it is far more complicated when others are involved. There is a third person in this relationship - Ed Richards, the chief executive of regulator Ofcom.
Richards, a very acceptable figure in the corridors of New Labour, has a big idea - the concept of the public-service publisher (PSP).
On the surface, nothing seems more reasonable than the setting up of a PSP to inject perhaps £150m a year into genres of public-service programmes that have been squeezed to the margins.
It certainly seems a good idea to those who would like to get their hands on the money, and culture secretary James Purnell and his boss will no doubt like the intellectual clarity of the proposal.
The danger is that it will get tangled up with a number of related notions - top-slicing the BBC licence fee and meeting Channel 4's 'funding gap' with public assistance.
On Monday, Channel 4 continued its campaign to remove any residual doubt that there might be a public service 'funding gap' by paying £28m for a 50% stake in Emap's music TV business - The Hits, The Box and Kerrang!
The problems for the BBC from a Richards-Brown axis is that the money for a PSP and/or propping up Channel 4's ambitions will be top-sliced from the BBC in the name of pluralism, and there will be no extra money in the system at all.
There are problems with such an approach. Who will commission PSP shows, where will they be shown and how big will audiences be? Arts Council dispensing of Lottery money for British films produced only turkeys and millions were wasted.
There is an awful lot of Brown stuff awaiting the BBC.