That's because presenter converts your powerpoint
presentation into a series of small Flash documents, which are
shown in a Flash shell (veiwer.swf). It may appear in an HTML
wrapper, but Breeze is pure Flash. And, of course, the fonts are
embedded in the Flash document, so they're not affected by your
brower's HTML settings.
As far as your desktop font size, have you tried changing it
in the display properties, under the "appearance" tab?
Cheers!
MarcTheAverage