In WB config set taskbar size to skin decides, I would guess it is set to small taskbar size and the content margins of the skin for the system tray are set to close together causing icons to not show.
I tried to reproduce the effect on my system by selecting "small taskbar". This made the taskbar thinner, but the icons were still there.
As the author of that skin, I'd like to know about any glitches. But it seems to be something else as PumkiN_KinG has tried other skins and had the same issue.