kpsewhere acts very strangely here. It looks as if the whole concept of
    kpsewhere flawed, maybe only in newer web2c/libkpathsea versions? 

I've never understood/maintained/looked at kpsewhere.
This is what I get in native TL (development):

$ kpsewhere texmf.cnf
/home/texlive/karl/Master/texmf/web2c/texmf.cnf
/home/texlive/karl/Master/texmf/web2c/texmf.cnf
/home/texlive/karl/Master/texmf/web2c/texmf.cnf
$

So I doubt the problem (whatever it is) is Debian-specific.

Perhaps I should mention that this year, I implemented a --all option
for kpsewhich, which will return duplicates within a single tree (which
kpsewhere was never intended to), as well as searching all trees.

If someone cares enough to improve kpsewhere, patches are welcome.
I don't plan to work on it myself.

karl



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