This one is hiding if you hover the mouse over another word.
I added comments for the new parts only, but there are some other minor changes - better grab the code again.

Code:
on ^*:HOTLINK:*:#: {
  var %nr = 1, %prefix
  while ($mid($prefix,%nr,1)) { var %prefix = $addtok(%prefix,$v1,44) | inc %nr }
  if ($remove($1, [ %prefix ,<,> ] ) ison $chan) { clonescanwindow $v1 $chan }

  ; mouse moving over another word in the channel window: hide clonecheck-window 
  elseif ($window($+(@clonecheck,$chr(160),*),1)) { window -h $v1 }

  halt
}

; the clonescan-and-show alias
alias -l clonescanwindow {

  ; store active window to a var 
  var %a = $active, %w = $+(@clonecheck,$chr(160),$2)

  ; create a new- or restore and rename the old clonecheck-window 
  if ($window($+(@clonecheck,$chr(160),*),1)) {
    renwin $v1 %w
    window -o %w
  }
  else { window -doCk0w0 +L %w -1 -1 280 55 }

  clear %w
  if ($ialchan($+(*!*@,$ial($1).host),$2,0) == 1) { aline 9 %w $chr(2) no clones $+ $chr(15) of $1 }
  else { aline 4 %w $chr(2) $calc($v1 -1) $iif(($v1 == 2),clone,clones) $+ $chr(15) of $1 }

  ; refocus stored active window
  window -a %a
}

menu @clonecheck* {
  close window "clonecheck" : window -c $active
}


... not that cunning, but I think it's ok.
Ah: it makes it quite... tricky to "grab" the window's title bar (to move it arround etc) laugh [hint: hold down left mouse button until you reach the window]

EDIT: now you edited your request *grin* - tomorow I'll have a look at it again smile