The applet's settings are different if the applet is present in multiple panels, for example, if you have multiple monitors. This can be verified by opening the dconf editor. In my case, having two panels with the dock in both, I have two entries for it, one under /org/mate/panel/objects/object-1 and another under /org/mate/panel/objects/object-14. The fact that the settings aren't synced can be checked by changing the color of the indicator icons in one of them, which does not change the color in the other instance.
I'm using the latest git revision, running on the GTK2 version of MATE under Arch Linux.
This is expected behavior and I think it should stay this way. Don't forget, it's the same behavior for the panel too. Changing the background on one panel doesn't change it on the other.
The applet's settings are different if the applet is present in multiple panels, for example, if you have multiple monitors. This can be verified by opening the dconf editor. In my case, having two panels with the dock in both, I have two entries for it, one under /org/mate/panel/objects/object-1 and another under /org/mate/panel/objects/object-14. The fact that the settings aren't synced can be checked by changing the color of the indicator icons in one of them, which does not change the color in the other instance.
I'm using the latest git revision, running on the GTK2 version of MATE under Arch Linux.