I'm unable to replicate your problem. Here's the code I'm using:
my $mw = MainWindow->new(-title=>"Foo!");
my $f = $mw->Frame(-width=>400, -height=>400)->pack;
print "Tk is $Tk::VERSION; Window id is ",$f->winfo('id'),"\n";
my $child = $mw->Toplevel(-title=>"Bar!",-use=>$f->winfo('id'));
..which tells me that Tk is 800.023; Window id is 0x2e00004 and pops up a window. Either your version of Tk is out of date or something, or there's something in the surrounding code which is making Tk go awry.
perl -pe '"I lo*`+$^X$\"$]!$/"=~m%(.*)%s;$_=$1;y^`+*^e v^#$&V"+@( NO CARRIER'