You don't appear to be passing a file-name to the scripts, therefore you are probably using fixed filenames, unless you are generating them in some way in the scripts. Therefore it is most likely that you are overwriting the files on each loop iteration.

A few other observations:
The loop is probably bettern written as:

for my $file (<*.tgz>))
{
    $tar1->read($file);
    ...
}
[download]

I don't see any error checking, anywhere. What if you cannot open the tar file? What if @filelist does not have the right number of files in it? What if any of the perl scripts fail? Some of these problems could cause your symptoms, possibily silently (depending on your scripts).