It's not failing because of the last; it's failing because you've aleady read to eof in IGUSERS.

Use a hash for the ignored users:

    open FH, "$workdir/ignoreusers"
        or die "Can't open $workdir/ignoreusers: $!";
    my %ignore;
    while (<FH>) {
        chomp;
        $ignore{$_}++;
    }
    close FH or die "Can't close ignoreusers: $!";
[download]

Then you can look up an ignored user like this:

    if ($ignore{$user}) {
        ## Ignore this user.
    }
[download]

In fact you could just stick this in your while loop:

    next if $ignore{$user};
[download]

Then you can get rid of *all* of that $matched stuff.