Have you, instead of toggling the visibility, toggled the zOrder of your modules, provided they have those bangs?
Meaning you want them on top.. so force them back on top by untopping them and retopping them (*gasp* pardon my language). For modules that lack separate on-bottom and on-top bangs, such as systray2, call !SystrayOnTop twice.

If modules' zOrder bangs are nonexistent, try the module WndMan.dll for its on-top bang..

You might be able to do all of this in a single !execute string.

Then you can try hooking this up to DesktopOnDisplayChange or jDeskOnRezChange in an unreleased version of jDesk.