wdb -- On Linux/KDE, it is possible that applications are restricted not to raise/lower any window. The application "Kontrollzentrum" (in English KDE probably "Control Center") has got a switch where this can be allowed or forbidden.
With my current Linux distribution Kanotix, this restriction was set. Tcl/Tk was affected such that the commands lower, raise did not work. In a Kanotix forum, I found the right hint. The complete solution was on my German desktop:
Kontrollzentrum -- Arbeitsfläche -- Fenstereigenschaften -- Vorbeugen gegen unerwünschte Aktivierung.
RS Wild guess: on eTcl / Windows/CE, raise alone has no effect, wm deiconify helps though...
LES on April 18 2006: I am running a Tk app without the title bar, removed with [wm overrideredirect . 1]. The effect of that is that the app stays on top of all other windows at all times (Linux/KDE). I tried adding lower . to it, but then the app disappears completely. I discovered that a few days ago and still haven't found a solution or explanation.