Version:           3.3.91 (using KDE KDE 3.5.4)
Installed from:    Gentoo Packages
Compiler:          i686-pc-linux-gnu-gcc (GCC) 4.1.1 (Gentoo 4.1.1-r1) 
OS:                Linux

Sometimes some of the menubar icons disappear. Mostly the "compile" or the "run" Icon from the buildbar disappear. I wasnt able to reproduce this yet, through it happens often, forcing me to restart kdevelop. 
However I am able to let the save-file icon disappear/dublicate on purpose. This is somehow related to the Code-Completion and the Switch Header/Implementation. It is reproduced as following:

You need to open an implementation-file (*.cc or *.cpp) whitch also has an existing header (same name but .h ending, im sure you know ;)) so that you can switch between them via hotkey (i dont know whats the default hotkey, but mine is <strg + s>).
Then you need to bring up an autocompletion popup. For example write "this->" and press <strg + space>, but any other will work too. 
Then switch back to the header-tab by pressing the hotkey for switch header/implementation. Most likely you will have two "save file" icons now. 
the "click right on editor" popup menu wont also work until you switch back. Sometimes other strange things will happen, like "blinking" tabs.

Here are some screenshots of my configuration and how the bug "looks":

http://666kb.com/i/ai86y1mi7u31sg64v.png 
This is *before* i press the hotkey for "switch Header/Implementation"

http://666kb.com/i/ai86zbasn4mcnqkun.png
This is *after* i pressed the hotkey another time to switch back. 
Note the to "disks" in the Menubar, and the two "bookmark"-entrys in the Menubar.

http://666kb.com/i/ai872y381grwmafin.png
Now i have pressed the hotkey another time and and the save-file icon is disappeared. Also the "bookmark"-entry is gone and opening a popup does not work. 

The Shortcut you need is under "C++ Support" -> "Switch Header/Implementation"
Speeking of hotkeys: if you "run" this bug several times your shortcut-menu will look like this: http://666kb.com/i/ai87icw4um3pahhxr.png


A quick fix would be to disable the hotkey when a autocompletion-popup is open,
like the popup-menu does, but i think theres a bug in the Menu/Icon bar as well, who needs fixing.
Maybe this bugreports helps you to find it.