I have not been able to reproduce this issue so far. If you copy mirc.exe and an empty mirc.ini to a new, empty folder and then run mirc.exe from there, are you able to reproduce the issue with a specific set of steps? For example, I am using the following script to create several query windows:

Code:
test {
  var %i = 0
  while (%i < 5) {
    var %name = test $+ %i
    query %name
    echo %name Hello Goodbye
    inc %i
  }
}

If you can describe a step by step method of reproducing the issue in a clean setup, using the query windows created by the above script, I will try to reproduce it here.