Try:

while (<DATA>) {
if (/regular files|archdone files/) {
local $, = "\n";
s/,//; print +(split)[2], $,;
$diff[++$i] = (split)[2];
}
}
print $diff[1]-$diff[2],"\n";
__DATA__

regular files  62,622    597.488G          641547379187
archdone files 62,535    597.008G          641032761295
[download]

Your code wasn't performing a subtraction. Also, as Roy mentioned the /^\d+/ wasn't matching.