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Adam: the problem is the way you ./configured CTB.
You need to use the following options:
./configure --host=arm-poky-linux-gnueabi --sysconfdir=/etc --prefix=/usr
In this case, the system cannot find the /etc/ folder because you didn't pass the correct --sysconfdir and it now searches in /usr/etc.
So a simple re-compile with those configure options should solve this issue with the desktop.
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