I have already found the problem and have viewed the first DjVu files on my reader. It seems to be much faster than the PDF viewer.
I had forgotten to remove the GConf configuration that caused CTB to be trying to load evince instead of my new plugin (took me a while to figure out, I tarred the whole / filesystem onto my SD card, then extracted it over an emulator image, and then copied /etc/network/* and /etc/hostname back from the original development image). After a rm -rf /home/root/.gconf it worked fine.
I'll first reinstall the firmware (1.7.1) on my DR1000 and then test some more, to make sure I haven't forgotten to include anything. Is it correct to assume that all files in / are replaced by a firmware update, except /home/root ?