It seems that initexmf doesn't follow for the order of
command line options. When install a new font package,
for example, and run:
initexmf --verbose --update-fndb --mkmaps
so that initexmf could integrate the new .map file to the
system fontdb, initexmf runs --mkmaps first followed by
--update-fndb. Thus a second run is needed.
I remember seeing similar problem when installing a new
font package some time ago using Update Wizard. It run:
initexmf --verbose --update-fndb --mklinks --mkmaps
the fontdb got updated first and then fndb. Even now
every time I run Update Wizard I still see the two dbs get
updated in that order.
I think it should follow the order of the command line
options. Another way is to change the default order so
that the fndb gets updated first followed by fontdb.