I had the same problem, but I managed to get around it. Here's what I did:
The installer seemed to be convinced that FFH was installed to C:\Games\Civ IV\Beyond the Sword\Mods, despite it actually being on the F: drive (same path otherwise). I'm not entirely sure why that was the case. At any rate, I simply created an otherwise empty path at c:\Games\Civ IV\Beyond the Sword\Mods, and dropped in a copy of my Fall from Heaven 2 040, then ran the installer.
It completed without a hitch, so I then copied the installed Fall Further 050 to the f: path, and the game runs just fine.
No clue why it makes me need to do it this way, but at least it worked. *shrugs*