I suspect this is a problem with "at" rather than with Perl.

system("at 17:00 echo \"go home\"");
system("at");
system("at 1 /delete");
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produces:

Added a new job with job ID = 1
Status ID   Day                     Time          Command Line
----------------------------------------------------------------------
+---------
        1   Next 20                 17:00         echo "go home"
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for me. But I do recall having a hard time getting certain types of quotes to not disappear w/ "at" jobs under WinNT and Perl wasn't creating the jobs.

You could always try:

system('at 12:00 program ""the.server.org:1234""')
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for increasing numbers of "s until it works.

        - tye (but my friends call me "Tye")