We have a 15" notebook with a very high res 1900x1200 display. My writer who took over this machine reset the resolution to 1680x1050 to make it more readable. She also bumped up the font to 125% of normal. Then we discovered that the PDFs produced by Flare were very odd looking: the characters were set far too wide apart--the kerning was awful. This puzzled us for a long time, as my machine, set up with the same software, fonts, and OS, produced correct-looking PDFs. I tried replacing the fonts, reinstalling Acrobat, reinstalling Flare--nothing worked. PDFs created from Word looked fine however. And there was nothing amiss in the Adobe Distiller settings.
After ignoring this issue for some months, I finally discovered that the 125% font magnification was the culprit! Evidently, this magnification caused the characters to "take up more room" when previewing the topic in Print mode in Flare, making it seem like fewer characters would fit on a line. But when the PDF was created, the actual fonts took up "less" room than the preview implied, so Flare simply spread apart the characters to match what the preview had shown!
So until MadCap addresses this problem, I urge everyone to not use the font magnification feature in Windows 7. This will cause unexpected output in PDF targets. Lowering the screen resolution seems to have no impact on the PDF though.