It sounds like you just want to make {1,5} not greedy to me.
$running_total =~ s/(\d{1,5}?)0*$/$1/;
Is this what you want?
update: Looking at your question again, perhaps your problem is also that you're doing a substitution (which I just parroted) and you really want to do something more like this:
$running_total = $1 if $running_total =~ /(\d{1,5}?)0*$/;
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