This also explains my duplicate lines in the log file

In a word; upgrade. At least threads & threads::shared. Preferably Perl also.

But these things are often out of our control :(

At a pinch; assuming that the quote means that the signal handler is being called separately on all the threads, add a check to only process the signal if you are the main thread. (Untested.):

sub handler {
    yield, return unless threads->tid == 0;
    ## Handle the signal
}
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