Meanwhile I've contacted Freescale and yes, the device initialization problem was my fault: the problem was, that after restarting Eclipse, I had open the DeviceInitialization.pe folder in the Project Packages view, which looked like a file and just double clicking on it opens just an XML file, so I didn't realized this the first time. Then double clicking on the CPU opens the device initialization again.
The Freescale support provided a beta version of the Bootloader GUI for me, which has still some bugs, but works on my Windows 64 platform. And they described, how to install the good old Code Warrior V6.3 on Windows 7 64bit: Just copy an installation from a 32 bit XP machine and run the regservers.bat in the bin directory of Code Warrior as an administrator. Now I don't have to mess with Eclipse for developing.