Your primary problem is that you have a colon (:) after PHM Away System when it's just a top-level label for several sublevel popups.
Code:
menu menubar,channel,nicklist,query {
  -
  PHM Away System
  .PHM Away Preferences: phmawaypref
  .Set PHM $iif($away,Back Mode,Away Now) : $iif($away,setbackphm,phmawaynowf)
  .Pager:{
    set %phmpagermsg69 $$?="Pager Message"
    set %phmpagernick69 $$?="Who To Page"
    ;  That long old ctcp pager thing goes here
  }
  .Read Pages: run NotePad.exe $+($scriptdir,page.txt)
  .Clear Pages: { 
    write -c $+($scriptdir,page.txt) Clearing all pages on $fulldate 
    echo -at ** Page file now cleared
  }
}