Canonical is the parent company of the Ubuntu GNU/Linux distribution.
CTO Matt Zimmerman, in a post on his blog, said he had been there in person when Shuttleworth gave his keynote at LinuxCon and had briefly spoken to his boss about the comment shortly after his talk.
"The remark in question was sexist, and although it may seem small in itself, it is representative of an attitude which is harmful to the community," Zimmerman wrote, having earlier clarified that he was speaking mainly "for myself, and in part on behalf of the Ubuntu community (not Canonical)."
As with all such posts on private blogs, the usual point-scoring exercise has begun in the comments that follow his post.
There is the occasional insightful take; for example Martin Krafft, a senior Debian developer, writes, in part: "I repeat myself when I claim that I am all for making OSS more friendly a place. I prefer to look at it from an egalitarian perspective.
"The way feminists approach the matter these days makes me wonder whether they want women to be treated special, or not. Obviously a feminist will say 'not special' (cf. egalitarianism), but I am beginning to doubt that."
How exactly Zimmerman's remarks will go down with Shuttleworth is difficult to say though it is fair to assume that the former knows his boss much better than anyone outside the company.
At least one senior FOSS personality told me that he expects Shuttleworth to issue an apology in the coming days.
It may be recalled that an open source consultant Kirrily Robert had asked Shuttleworth to apologise for the remark without having even viewed the Canonical head's keynote, but been satisfied to demand an apology based on hearsay.
My take on Robert's unreasonable reaction has earned me some flak from a gent named Chris Ball - but then he is the lead software engineer for One Laptop Per Child and given the drubbing that I have meted out to that project I don't expect anyone there to even give me the time of day. Objectivity is not a strong suit when it comes to the OLPC.
Yet nobody has told us what has caused many people to take offence and others to argue that there was nothing wrong with what Shuttleworth said.
His keynote came at the end of a day - close to what he called beer time - and ran for about 35 minutes. Towards the end of his discourse, he was talking about how various subsystems could be made to work seamlessly.
He made reference to Till Kampeter, who has done yeoman work in getting printers to work with Linux, no matter what their ancestry, and then said that if people could get various other subsystems like USB and Wi-Fi to work in the same way "we would have less trouble explaining to girls what we do."
He didn't say that it was more difficult to explain something to a girl than to a boy; men often try to impress women by making out their jobs to be something very important and his remark seems to fit in with that. It doesn't happen the other way round.
In the furore that has followed Robert's outburst, nobody bothered to find out what Shuttleworth said in his keynote.
He talked at length about trying to get distributions to sing in tune when it came to releases, something he has been discussing for a while now.
Shuttleworth also spoke about the need to bring better design into the Linux space, so that end users would benefit and the operating system as a whole would end up being number one.
His talk was one by a future leader of the free software world, one who understands the greater needs that free software can serve, not just the immediate need for an alternative operating system.
Yet people have chosen to crucify him for 11 words in a 35-minute speech. Do I hear the words Salem, Massachusetts, somewhere?