You shouldn't have to do anything with Radius to take care of this problem.
The only time we ever ran into a problem with an extra prompt was when we
acquired another ISP that was unix based, we had to contend with rlogin
users getting an extra password prompt. This was taken care of by adding
the IP address of the authenticating NAS into some .conf file on the unix
system that they were rloging into. As for PPP users dialing up, an
additional prompt of any kind has never shown up when people connected
manually or with scripts (only a tiny handful do this to begin with). I
never had to make any adjustments to our Maxes or anything in the radius
settings for the PPP account-type in our database (using RadiusNT).