It is instructive to look at what the flip-flop operator actually generates. Consider:

use strict;
use warnings;

my $str = '[][ab]c[]d';

for my $chr (split '', $str) {
    my $result = $chr eq '[' .. $chr eq ']';
    printf "%-2s %s\n", $chr, $result;
}
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Prints:

[  1
]  2E0
[  1
a  2
b  3
]  4E0
c  
[  1
]  2E0
d
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Note the iteration count for 'true' and that the last iteration has a trailing 'E0'. Your 'missing blank line' problem is just like the '][' case above - you need to either retest the ending condition and exclude it, or you can save the flip-flop result and test that.

If you haven't seen it already, you may find Flipin good, or a total flop? of interest too.