Yes, there should be nothing "local" in the Makefile if you do a search. Most probably pkg-config isn't right, but this should not happen in Debian. Paths aren't the problem here, though. Try:
./configure --prefix=/usr \
--without-jack-dbus
I've read there's a problem with jack1+dbus. Sorry I can't be of more qualified help, but an e-mail to a Debian package maintainer, lash and jack dev will definitely shed light.
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