The error is on while loop. It loops all users in the channel, so if the channel has 100 users then it will repeats 100 times as well.

Code:
on admin:TEXT:.fn*:#:{
  var %a = 1, %b = 0, %c = $ticks
  msg # 1User List Scan Started..
  while ($read(users.txt,w,$+(*,$2-,*),%a)) {
    msg # $v1
    var %a $calc($readn + 1)
    inc %b
  }
  msg # 1 %b $iif(%b = 1,user found,users found) 0›1 $calc(($ticks - %c) / 1000) Secs.
}

I dont know what is inside your users.txt files, so the code just msg plain output.
- Not tested.