Just to update - I had to revisit this block of code recently with slightly more experience. Wrapping the code in an eval and viewing the resulting $@ revealed that the mkdir was in fact firing twice in immediate succession, producing the 501 error on the second attempt. 
$ftp->cwd($i2) or die "change directory $i2: ".$ftp->message." / ".$ft
+p->code;
my @nfiles = $ftp->dir;
if(grep {$_ eq $i3} @nfiles){
die "make $i3: already exists";
} else {
$ftp->mkdir($i3) or die "make directory ".$ftp->code;
}

[download]
Although still not obvious to me exactly where, it looks like code elsewhere was looping over the mkdir without being caught, so I rewrote, removing the eval/dies, which seems to behave as expected. 
push @errs,"cannot change directory from $ftp->pwd to i2: $ftp->messag
+e" unless $ftp->cwd($i2);
my @nfiles = $ftp->dir;
push @errs,"cannot list directory $ftp->pwd: $ftp->message" unless @nf
+iles;
push @errs,"directory $n2 already exists in $ftp->pwd: $ftp->message" 
+if grep {$_ eq $n2} @nfiles;
push @errs,"cannot make directory $n2 in $ftp->pwd: $ftp->message $ftp
+->code" unless $ftp->mkdir($n2);

$ftp->quit;
if(@errs){ print join "<br />",@errs; }

[download]

In reply to Re^2: NET::ftp mkdir succeeds but then dies with 501? by rjc_thatsthat
in thread NET::ftp mkdir succeeds but then dies with 501? by rjc_thatsthat

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