The down side is that it is not only a single character repeated ('AAAA'), but short repeating sequences ('ACTACTACT') that can be missed or truncated. The up side is that for bioMan's problem a minimum match quanta of 128 is probably optimum and I'd guess that that is long enough to be unlikely to be a problem.
At this time I've not thought of a fast way of dealing with the issue and am somewhat inclined to ignore it unless someone can convince me that this is really useful code, but needs this bug fixed.
Perl is Huffman encoded by design.
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