How are you parsing/storing your CGI data? I had the same problem you're describing before I started frequenting Perlmonks. I used the $cgi->parm('var') methods but I used eval to create variables and assign their corresponding values:

The following code is BAD! don't use it!

sub doGetCGIvars {
    my $VarName;
    my $query = new CGI;
    foreach $VarName ($query->param) {
       $assign = "\$$VarName = '" . $query->param($VarName) . "'";
       &UnTaint($assign);
       eval($assign);
    }
}
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Why is this bad? Because any param that has a single quote in it will screw things up. Likewise, if I had used the following:

$assign = "\$$VarName = \"" . $query->param($VarName) . '"';
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params containing a doublequote would screw things up. Instead, use one of the saner methods recommended by Ovid in his reply to Best way to parse CGI params and check out his CGI Course for more pointers and other reasons why you shouldn't use methods like the ones above to parse/store cgi data.

--Jim