This seems like the most likely explanation to me.

My initial guess was that the problem was output buffering coupled with something causing the script to hang toward the end. But testing that theory doesn't show the buffered output being flushed for such a case.

One thing that I find very annoying is that, by default, Windows considers very small mouse motions to be "drags". Since the typical configuration has the button mounted on a movable mouse, it is quite hard for me to consistently press a mouse button without moving the mouse pointer a couple of pixels. So, by default, my mouse "clicks" often become "drags", which have results much different than were desired.

So every Windows system (with a mouse) that I end up working with for more than a few hours get the following changes applied:

my $Reg;
use Win32::TieRegistry( TiedRef => \$Reg, Delimiter => "/", ArrayValue
+s => 1 );
$Reg->{"CUser/Control Panel/Desktop//DragHeight"}= 10;
$Reg->{"CUser/Control Panel/Desktop//DragWidth"}= 10;
$Reg->{"CUser/Control Panel/Mouse//DoubleClickHeight"}= 10;
$Reg->{"CUser/Control Panel/Mouse//DoubleClickWidth"}= 10;
[download]

(They default to just 4 pixels -- and I think some of them used to default to just 2 pixels.)

A similar change might make your "bug" less frequent.