Synaptic is run as root. It seems that you have only modified the fonts.conf of your normal user. You would have to a system wide change or change the fonts.conf of root too.
** Changed in: synaptic (Ubuntu) Status: Unconfirmed => Rejected -- synaptic package manager does not follow user font settings https://launchpad.net/bugs/64687 -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs