While installing via apt-get, every such situation is presented with question what to do (replace old config with new config from package and append .dpkg-old to old version, etc), so using this way, all such problems are avoided. I have habit of doing so to get an idea what scripts/configs CSSU replaces, to re-merge my custom changes, after installation.

Still, CSSU's prefered method of update is via HAM - I suspect that HAM may have (hardcoded) some stupid idea of what to do with new configs by default?

Using fapman (FAM), default hardcoded action was to use new (from package) config file, so, ironically, FAM users aren't hit by that problems during installation of CSSU [and it was reason why I switched to manually update via (f)apt-get - harder to keep track on what got changed, otherwise].

/Estel