Some more info: it seems that the missing entries in depend file are not the cause of the problem but an effect. I replaced the depend file with an earlier version (which had all files included) and C::B is ignoring it: no rebuild when changing any of the headers.
... and I don't think there is much more I can do. I tried most things I can think of... I think this will need an analysis of the source code.
there is something, you totally ignore in your posts.
It works on some (many ?, most ?) systems, windows and linux.
So it still might be an issue on your system(s).
Can you please check the timestamps of the source-, header- and object-files, before and after a normal build and a full rebuild ?