This can easily happen when Perl buffers some data instead of flushing it to disk. A second file handle opened to a file can't see that buffered data. Your solution of using lexical filehandles won't solve every case, for example the following:

sub write_stuff {
    open my $fh, '>>', $logfilename or die "Can't append to '$logfilen
+ame': $!";
    ...
    check_stuff();
    ...
};

sub check_stuff {
    open my $fh, '<', $logfilename or die "Can't read '$logfilename': 
+$!";
    while (<$fh>) {
        ...
    };
};
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(also see Suffering From Buffering)