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.