I have the same problem since a couple of days too.
Workaround:
gsettings set org.gnome.desktop.default-applications.terminal exec
gnome-terminal
It is already set to gnome-terminal for me (according to dconf-editor).
I don't know if it is related but when I launch a script from nautilus, and
click on « launch in a terminal », the terminal opens in the correct directory
but the script is not executed.
I think the problem occurred after I updated those packages :
fonts-liberation (1.07.2-5) to 1.07.2-6
gir1.2-gdesktopenums-3.0 (3.4.2-1) to 3.4.2-2
gir1.2-gmenu-3.0 (3.4.2-3) to 3.4.2-4
gnome-menus (3.4.2-3) to 3.4.2-4
gnome-system-log (3.4.1-2) to 3.4.1-3
gsettings-desktop-schemas (3.4.2-1) to 3.4.2-2
iso-codes (3.39-1) to 3.40-1
libgnome-menu-3-0 (3.4.2-3) to 3.4.2-4
libopenjpeg2 (1.3+dfsg-4.1) to 1.3+dfsg-4.6
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