I already included this information in my thread about replacing Caja with Nemo, but I felt the information is going to be missed if I don't include this bit in its own separate thread.
With the release of GTK 3, came also some location changes for some items. Where legacy GTK file managers store bookmarks in
~/.gtk-bookmarks, GTK 3 file managers will (or at least should) store files in
Where the files are isn't important, how they are formatted is; They're essentially the same file. You can even copy contents to and from these files, but if you want to make these bookmarks universal and appear in modern GTK applications, you need to delete one, and symbolically link the other. Since MATE is generally a GTK 2 DE, doing this should prevent issues when you change your mind about having GTK 3 applications in your installation (or at least, remove any programs such as nemo which rely on it);
rm -rf ~/.config/gtk-3.0/bookmarks
ln -s ~/.gtk-bookmarks ~/.config/gtk-3.0/bookmarks
From thereon after, bookmarks made in GTK 3 apps such as Nemo will be made in the same space GTK 2 bookmarks exist, which will also resolve all issues related to legacy programs not seeing GTK 3 bookmarks.