Probably because Synaptic is a GTK application and you need to install additional packages to control the look&feel of GTK apps under KDE. I have two packages installed for this purpose: kde-gtk-config and kde-config-gtk (yeah, I know - someone really worked hard to name them lol).
However, there seems to be a general problem with these settings because of kde-defaults package - when you change and apply font settings for both GTK and KDE apps, they don't stick. You have to manually edit the files in /usr/share/mintkde-default-settings. KDE GTK config creates a file there called dot-gtkrc-2.0-kde4. I changed the font settings in that file and then it finally had effect on both Synaptic and Pidgin (probably the only GTK apps I use).
I hope this info helps you