Lots of stuff installs into /usr/local; this needs --prefix=/usr in XFCE_CONFIG
Whoops. This was caused by my recent fix for the file collision. Basically, I had patched a Makefile.am, so had to regenerate stuff... and the only thing that seemed to work was using xfce4-dev-tools' xdt-autogen, which is a wrapper around configure. So, either need to get all the appropriate args to xdt-autogen that would normally be applied with econf, or need to find another way of regenerating stuff.
Well, as said --prefix=/usr fixed the issue, but I guess you are into something more generic here...
Fixed for real now in -r3. xdt-autogen is used for generation, but not configuring. econf is then used, so it gets all the right args.