I think the problem may be with your naming scheme. As opposed to naming the select box something like "input", try naming it:

input[];

For the full example:
    <form>
       <select NAME="input[]" SIZE=3 MULTIPLE>
          <option VALUE="opt1">option1
          <option VALUE="opt2">option2
          <option SELECTED VALUE="opt3">option3
       </select>
    </form>
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And then when it gets to your Perl script, you can treat it as an array. Otherwise, your Perl script really does only see it as one value.
-Eric

UPDATE Okay, maybe it's time to kick myself for having a PHP background before I came around to the Perl world :-)

However, what would the proper method be in this scenerio -- If I used HTML::Template to build my template, and CGI.pm to process them.. in that case, what would be the proper thing to name the SELECT element?

a.
<select name="myname" multiple>

b.
<select name="myname[]" multiple>
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Thanks! :-)