if $active != status window

why not the contrary

on *:input:*:{
  if ($left($1,1) != /) && ($active != status window) && (%font) {
    haltdef
    msg $active %font
  }
}

menu menubar,channel,query {
  .Fonts
  ..Blue :set %font 12%0,12% 2%12,2% 1%2,1%0 $!1-  2%1,2% 12%2,12% 0%12,0%
  ..Red :set %font 4%0,4% 5%4,5% 1%5,1%0 $!1- 5%1,5% 4%5,4% 0%4,0%
  ..Green :set %font 9%0,9% 3%9,3% 1%3,1%0 $!1- 3%1,3% 9%3,9% 0%9,0%
  ..Pink :set %font 13%0,13% 6%13,6% 1%6,1%0 $!1- 6%1,6% 13%6,13% 0%13,0%
  ..Off :unset %font
}