Using local $var seems to be the fix for such problems. Although it may/may not work with mod_perl, it seems to work fine within the FCGI loop.

use FCGI;

while (FCGI::accept >= 0) {

    local $cnt;
    local $last_elapsed;
    
    ###############
    &http(0);
    &head();
    &t('');
    print "OK";
    &t('');
    &t('');
    
    my $cc;
    while ($cc < 1000){
      &test;
        $cc++;
    }    
}

sub test(){
    print "CNT: $cnt";
    $cnt++;
}
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