I'm not sure what's going on, from your description, but I'm guessing you need to escape what's in $joined. CGI has an escapeHTML function that would help with that.

use CGI;

print qq{<form action='/cgi-bin/opal/display_seview.cgi' method='post'
+ target='new'>
<input type='hidden' name='text' value='@{ [ CGI->escapeHTML($joined) 
+] }'/>
<input type='hidden' name='header' value='@{ [ CGI->escapeHTML($query)
+ ] }'/>
<input type='hidden' name='sequence' value='@{ [ CGI->escapeHTML($whol
+e_sequence) ] }'/>
<input type='submit' value='View Applet in new window'/></form>
};
[download]

I'd probably use the the function available for making hidden fields, though:

use CGI;

print qq{<form action='/cgi-bin/opal/display_seview.cgi' method='post'
+ target='new'>};
print CGI->hidden( 'text',     $joined );
print CGI->hidden( 'header',   $query );
print CGI->hidden( 'sequence', $whole_sequence );
print qq{<input type='submit' value='View Applet in new window'/></for
+m>};
[download]

CGI->hidden does the escaping for you (at least when I tried it).