Comment 3 for bug 968173

Hm... did you by any chance increase your default system-font's size? Or is your gnome-settings-daemon not running (this can also cause an implicity switch to default/larger font-size)?

Since notify-osd takes the default system-font-size into account - for calculating its size (being EM-based to be resulution-independent) - a jump in size can happen if the above mentioned conditions are met.