Ok, I figured it out. There is actually a simple fix for it:
just call this
panel_applet_set_background_widget(applet, GTK_WIDGET(applet));
//passing applet for the first and second parameter
when the applet is being initialized.
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https://bugs.launchpad.net/bugs/725584
Title:
Some gnome-panel Applets still use GTK theme's panel-background, even
if "use system theme" is not selected
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