I've found the problem now. If this bug ever appears again the following 
addition would fix it:
In file cpufreq-applet.c at line 881 add the following line:
    if (0 == label_size) return;
Then compile and install the new applet.
The problem source is that gnome sometimes calls the callback- and 
init-functions in the wrong order.

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cpufreq applet doesn't draw anything (white square) in gnome-panel
https://bugs.launchpad.net/bugs/267047
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