CB doesn't go onto the task bar until it is completely finished all it's start up tasks.
But that is perfectly normal, it is supposed to do that
To avoid mindless overdraw, we do not show the main frame until everything is initialised. The splash screen does not show in the task bar, but this, too, is intentional.
If you look closely at Code::Blocks RC2 (which does not retain the main window), you see that the complete UI is redrawn at least 20 times during startup. wxWidgets is particularly braindead when it comes to event handling, especially regarding UI updates. In fact, I often wonder that despite this, Code::Blocks is still usable at all.
If you are in for a good laugh, set a breakpoint in some function handling UpdateUI events, and count how many times it is called if you just move your mouse a tiny bit. For example, if you move your mouse over the middle of the editor (no way near the menu bar), you can be lucky enough to get 6-8 UpdateUI events for the file and the edit menu. Luckily, you have plenty of CPU cycles to burn
Nota bene: Actually, this might be one reason for the high CPU load problems reported with Xorg.