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Just like the tile suggests, When i use the custom style for panels, it does not override the font-family and font-size of the pane being styled (Both Header and body) in bartik theme, though the styling is applied in the preview mode. Other settings like background color are applied except the font-size and font-family attributes. Switching to garland theme, problem goes away. This has caused me to be using a lot of CSS hack to style the output of the panel.
To reproduce: use bartik theme, enable panels and CTools stylizer sub-module, create a panel page, add a drupal block to any region on the page, choose "custom settings", Change the header and/or body font-family and font-size, change other settings you desire e.g background color, preview the applied settings to make sure everything displays as expected, then save. Go to the created page, every setting made on the settings page to the region is applied except the font-size and font-family, which displays with the default bartik theme title font-size and font-family.
its a shame considering that bartik is the default drupal 7 theme.
Note: i also updated ctools to current dev version, still problem persists.