I reported it here: http://tracker.luatex.org/view.php?id=965
I'm glad Luigi could eventually reproduce the problem.
Why luatex loads different files depending from which directory it is
run?
I cannot explain anything about luatex behavior, which is (especially at
the moment) in a constant state of flux.
Is it something in TeX Live that causes this difference in behavior,
It is nothing in TeX Live, as far as I know. Nothing in TL in this
regard has changed, in any case.
or it is the problem with luatex?
I suppose so. All I can suggest is to report it to them. -k
