Now that I am “playing” with a Fedora 24 in VirtualBox, I found out there is an issue with GTK 3.20 
It has been widely discussed during the last months on the internet as most of the themes (even Adwaita, default one) are broken.
It seems it has nothing to do with Synfig but GTK version (I was under F23/GTK 3.18).
Use another GTK Theme
As a workaround, you can try to install another theme and select it instead of Adwaita.
On F24 (gnome), I installed breeze-gtk theme (sudo dnf install breeze-gtk*)
GNOME
From the terminal invoke gnome-tweak-tool, then select GTK+ appearance as Breeze (Light or Dark, as you wish 
)
You will surely have to modify the Interface Font Name/Size (see the link on the top of this post for a settings example)
LXDE/Openbox
You need to edit /home/username/.config/lxsession/LXDE/desktop.conf
[GTK]
sNet/ThemeName=Breeze
With an environement variable/desktop file
A last possibility is to do a .sh file (with execution premission) containing a reference to the expected GTK_THEME.
It can be done this way per application.
(And you can add an entry on your desktop pointing to it as well, sere here)
Hoping this will help 
