Think carefully what the script is doing:

• You get your text to analyze with $text = Win32::Clipboard::GetText();
• You are assigning the variable $text to the variable $zoektekst (completely useless, use your preferred variable in the first place: $zoektekst=Win32::Clipboard::GetText();
• While the string in $zoektekst is not empty you will be looping. while ($zoektekst) {
• If you match that regular expression, you copy the match in the $_ variable, delete one part and print another. The problem is that your substitution is made in the variable $_ that holds a copy of the previous match ($_=$&), but you are not changing the original variable $zoektekst at all. So, in the next iteration of the while loop, $zoektekst has the same content. You should be written:

  $zoektekst=~s%(d{13})\s+CG1%%;
  print $1;
  [download]

• The same for the next if

Hope this helps

citromatik

Update: Be sure you provide an exit to the while loop.