Immortal Late, but if I had to guess, it would seem that those icons are of a different type. Let me explain.
Every icon in the system tray is a separate borderless window, embedded in the tray. Most of these windows support transparent backgrounds, but some of them don't, like the two you're seeing. Without the ability to set a transparent background, the window can't be properly drawn on top of the panel.
Carbontray, like the old tray, attempts to rectify this by setting the background of the window to the color of the panel. As you've noticed, this works fine if the panel is opaque, but if the panel is transparent then you get those panel-colored squares. Without modification of the application itself, there's nothing I can do on the panel side (that I know of) to force those windows to support transparency.
