Well, for what it's worth, I just nuked my installation and downloaded the same thing minus ARP/wARP, and now I have the same header as you reported.  Will continue digging tomorrow, but I suspect that either the updates will eventually fix the problem, or something has changed in the installer (although using an older version of the monomer library seems like a weird choice).

Also note that you can download the monomer library as a separate package from Garib Murshudov's home page:

http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/  [ click "software" --> "Refmac5" --> "Dictionary of ligands" ]

and this looks like it is formatted correctly.

-Nat