Most likely, the delay is when shutting down Powerpoint as $ppt goes out of scope.

You can test this theory by explicitly clearing out $ppt yourself:

$presentation->SaveAs("SAVED_" . $filename);
$presentation->Close;
undef $ppt; # Clean up Powerpoint
$mw->messageBox (-title => "message", -message=>"DONE!", -icon=> 'info
+');
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There is very little way around this, but if you plan to convert more than a single presentation in one go, it might make sense to declare $ppt as a global variable and keep it around:

our $ppt;
sub save_PPT {
# ...
$ppt ||= Win32::OLE->GetActiveObject('PowerPoint.Application');
# ... and also later:
$ppt ||= Win32::OLE->new(
            'PowerPoint.Application', sub { $_[0]->Quit }
        ) or return 'error';
# ---
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