Seems like some plugins like time-out and mail watcher is not using a fully transparent background around the icon on the panel when panel preferences apperance style is set to system style. It background for the plugins is slightly more light grey then the rest of the panel. I am testing in VirtualBox.
Also the plugin icon on the panel for these plugin does not follow the panel preference to select the fixed icon size manually in apperance tab in case that can help.
If in panel preferences apperance tab i make the panel transparent with the slider to 0 the time-out and mail watcher icons will not become transparent. So i guess some plugins do not support transparency.
I would suggest you submit bugreports against those plugins that misbehave specifically. Unfortunately both of them are not the best-maintained, up-to-date panel plugins, but maybe your reports will trigger someone to pick them up (maybe yourself? :)). In any case, not a bugreport that's relevant for the panel.