Testing this on Fedora 17, what I've found is similar. If I configure using "--prefix=/usr", build out of tree and then do "make install DESTDIR=$PWD/temp", I see the Perl bindings being installed to /usr/local/usr/lib64/perl5/... similar to what's reported here.
I modified the bindings/qpid/Makefile.am as follows:
@@ -54,7 +54,7 @@ all-local: perl/Makefile
cd perl ; \
- $(MAKE) pure_install DESTDIR=$(prefix) ; \
+ $(MAKE) pure_install ; \
and redid the whole install. Now I see the files that were previously being installed to /usr/local/usr/lib64 properly being installed into the same tree as the rest of Qpid.
Please test the attached patch and, if it works for you, I'll push it.