My guess is that their recruiting software doesn't handle PDFs correctly. I recently went through a job search and was dumbfounded by the number of places that would only take a Word document.
It's that simple.
To put it another way, you're talking about spending $20k+ on the job search itself, then $1-2 million on the employee across his tenure. Finding the right candidate is important. Don't treat me like a temp from ManPower.
A firm that demands my adherence to arbitrary rules before they'll even look at my marketing flyer is not a firm I want to work for. It reflects an attitude I do not appreciate.
It doesn't make you a staffer from ManPower. The CEO probably submitted a Word resume.
You, as an individual, are free to apply to those jobs with a Word resume. I won't bother. I will be absent from their candidate pool. In my book, that is very much not a problem.
The CEO probably doesn't even have a resume in the sense that you're thinking of. He is playing a different game entirely, where all decisionmaking authority rests with a handful of identifiable people who he is selling directly. You want to be playing his game.
It's 2011, the efforts to boycott Microsoft have failed, the world is tooled to use Word for documents and Excel for lists and basic numerics. Adapt or suffer the consequences.